hello experts.
I have a question to you...
I'm doing recon-all stage... but errors showed up (fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve greve@nmr.mgh.harvard.edu:
don't use .hdr. When you have a .hdr/.img pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote:
hello, experts I have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001
and then error occured....
ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015
For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Specify something for --seg. It just needs to be a surface overlay of the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote:
Hello doug
i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' then, error occured --> ERROR: must specify a segmentation volume
2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>:
don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 On 8/26/15 9:22 PM, A-reum Min wrote:Hello developer, I have some question to you. How can i get the significant vertices value using Qdec result? When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 --avgwf out.dat', then error ouccured --> ERROR : Option out.dat unknown. So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. How can i fix it? 2015-08-25 23:41 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: On 8/25/15 9:35 AM, A-reum Min wrote:Hello developers I have some question to you. 1.In fig.png, how many vertices were composed of cluster at least?I'm not sure what you mean. it does not look like there are any clusters there2. How to change Area Threshold(fig.png)?The area is controlled by the clusterwise threshold (--cwp) to mri_glmfit-sim3. How to change CSD thresh(fig.png)?That is controlled by the threshold when specifying "--cache threshold sign" to mri_glmfit-sim4. What is the difference between two words(Area Threshold, CSD thresh)?One is the cluster-pvalue and the other is the cluster-forming thershold5. What is the exactly mean two words(Area Threshold, CSD thresh)?See aboveThank you 2015-08-12 23:23 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu:
On 08/10/2015 10:06 PM, A-reum Min wrote: > HI expert ! > > My name is Areum. I have some question to you. > > 1. Does FreeSurfer offer a effect size? if that offer, how can i use > effect size? > If you're doing a group analysis, you can compute fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o glmdir/contrast/effectsize.mgh > > 2. I was wondering about the stats.dat file in stats_table (in Qdec > folder). > > Stats.dat file’s value mean that each area’s average (include whole > vertex) or each > > area’s average (only significant vertex)? > what stats.dat? if subject/stats/lh.aparc.stats, then the area is the total area for the ROI > > 3. Can I get whole vertex value or significant vertex value? Because, > I want to > > compare two groups correlation using SPSS. In addition, I want to compare > > thickness, volume and surface area correlation within the one group > using SPSS. > You can extract a given vertex with mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf vertexno.dat vertexno.dat will be a text file with number of rows equalt to thge number of subjects where the value is the data from the given (0-based) vertex no. y.mgh is the input to mri_glmfit > > 4. I currently use the default cluster size(significant area threshold > is 0mm^2). So, I > > want to control cluster size larger than default cluster size. How can > I control the > > cluster size? > I don't know what you mean. > > 5. In FreeSurfer manual, GLM and Qdec have a same results. But when I > use the > > both(GLM, Qdec) group analysis program results are not same. What is > differences > > between two analysis program? How can I get same result while GLM and > Qdec? > No way to know unless you tell us the specifics of what you did > > 6. How can I get surface area and volume using GLM(group analysis > program)? > surface area and volume are outputs of recon-all, not glm > > > plz reply to me > > > 2015-08-10 21:35 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com: > > Hello developer~ > > I have some questions to you. > > 1. Does FreeSurfer offer a effect size? if that offer, how can i > use effect size? > > 2. I was wondering about the stats.dat file in stats_table (in > Qdec folder). > > Stats.dat file’s value mean that each area’s average (include > whole vertex) or each > > area’s average (only significant vertex)? > > 3. Can I get whole vertex value or significant vertex value? > Because, I want to > > compare two groups correlation using SPSS. In addition, I want to > compare > > thickness, volume and surface area correlation within the one > group using SPSS. > > 4. I currently use the default cluster size(significant area > threshold is 0mm^2). So, I > > want to control cluster size larger than default cluster size. How > can I control the > > cluster size? > > 5. In FreeSurfer manual, GLM and Qdec have a same results. But > when I use the > > both(GLM, Qdec) group analysis program results are not same. What > is differences > > between two analysis program? How can I get same result while GLM > and Qdec? > > 6. How can I get surface area and volume using GLM(group analysis > program)? > > > thanks for your help > > > 2015-07-27 14:28 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>: > > Hello bruce > > I solve this problem(12.png) > > Thank you > > 2015-07-27 13:03 GMT+09:00 dgw <dgwakeman@gmail.com mailto:dgwakeman@gmail.com > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com>>: > > Hi A-reum, > > I think you may be able to get a faster response if you > include some > details about your setup: I would start with the following: > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > and run bugr. > > hth > D > > On 7/26/15 5:17 PM, A-reum Min wrote: > > Hi, Bruce > > > > When i use a Qdec, this message(12.png) show up.. > > How can i solve this problem? > > > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>: > > > > 1. No, each subject has a different #. You can map > to fsaverage > > (this is what -qcache does if you specify it for > recon-all), then > > they will have the same #. > > > > 2. What result data do you mean? > > > > 3. Yes, although I'll leave the details to Doug > (since I don't > > remember how his cluster code works). > > > > 4. The significance doesn't depend on the cluster > size unless you do > > multiple comparison corrections (and even then only > if you do them a > > certain way) > > > > cheers > > Bruce > > > > > > On Thu, 23 Jul 2015, A-reum Min wrote: > > > > HELLO developer > > I have some question to you.. > > > > 1. Every patient is given to the same number > of vertex? > > > > 2. When i use a Qdec, How can I get
the
> subject result data? > > > > 3. Could i get the significantvertex’s
> number, extent of the > > significant area and gray matter volume? > > > > 4. Is it significant blue color which how > many connected > > vertex? > > > > > > 2015-05-29 2:03 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>:
> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treat the Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > age range is 12years~24years/ > > all subjects are adolescent. > > and no outlier in age range.. so.. age > (continuous factor) does not > > nasessart? > > > > > > 2015-05-29 1:19 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>:
> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treat the Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > > > > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > I'm glad it worked out > > Bruce > > On Sun, 5 Apr 2015, A-reum Min wrote: > > > > Hello Bruce~ > > You're right.. my PISA dicom file > header > > is too short > > so, freesurfer didn't read it. > > > > Therefore I use another subjects dicom > > file and then freesurfer read it! > > > > thank you for u r adavice to me. > > > > I really appreciate u > > > > 2015-04-05 7:08 GMT+09:00 Bruce Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > the problem is that newer > versions > > of scanner software compress > > dicoms and the version of FS you > > have doesn't know how to read > > it. So you need to decompress > them > > before passing them to > > recon-all > > > > cheers > > Bruce > > On Sun, 5 Apr 2015, A-reum Min > > wrote: > > > > Hello developer~ > > > > Can you summarize what the > > problem is? > > ==> > > my problem is recon-all -i > > didn't working... > > so, if i type the recon-all > > -i~then show up theses > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, see > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 GNU/Linux > > > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > then, i click the > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > Are you trying to read > > compressed dicom? > > ==> > > Am i trying to read > > compressed dicom? > > I send my 10071579.dicom(i > > use this) to you, > > using -i, convert the dicom > > file to mgh file. i just > > know that dicom file > > convert to mgz format using > > -i /my data path > > Is it right..?? > > > > > > If so, Can you try running > > dcmdjpeg on it to create > > a new (uncompressed) > > series and give that to > > recon-all? > > ==> (actually, i didn't > > understand your sentence > > means perfectly..) > > zeke > > > tomeaurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c
> > > > en > > t > > os6_x86_64/dcmdjpeg.fs) > > and then, replace my > > existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs file. > > Also, make sure it is set to > > executable by typing > > the following in a > > terminal window: > > $> chmod a+x > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > > > 2015-04-05 2:30 GMT+09:00 > > Bruce Fischl > > > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > sorry, I'm coming into > > this late. Can you > > summarize what the > > problem is? Are you > > trying to read compressed > > dicom? If so, can > > you try running > > dcmdjpeg on it to create a new > > (uncompressed) > > series and give that > > to recon-all? > > > > cheers > > Bruec > > > > > > > > On Sat, 4 Apr 2015, > > A-reum Min wrote: > > > > Hello > > developers.. > > > > i type the > > recon-all -i~then show up > > theses > > > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 > > UTC 2014 x86_64 > > x86_64 x86_64 GNU/Linux > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such file or > > directory > > > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > error is occured > > (a little differntly..) > > then, i click > > the > > > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such file or > > directory > > > > i'm so sorry..to > > bother you.. > > > > > > > > 2015-04-04 9:21 > > GMT+09:00 A-reum Min > > > > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: > > hello > > > > i type the > > recon-all -i~ > > then show up > > theses > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > > > ERROR: 32256, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out > > for more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 UTC > > 2014 x86_64 x86_64 x86_64 > > GNU/Linux > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > the error is > > occured (a little > > differntly..) > > then, i click > > the > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, > > show iuo these > > > > sh: > > > > /usr/local/freesurfer/bin/dcmdjpeg.fs: > > > > /lib/ld-linux.so.2: bad ELF > > interpreter: No > > such file or directory > > > > plz help me > > 2015-04-04 4:12 > > GMT+09:00 > > > > <zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> > > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>>>: > > A-reum, > > > > Please > > download the following > > file: > > > > >ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_
> > > > > > > > > > x86_64/dcmdjpeg.fs > > > > And > > replace your existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > file with > > the > > one from > > the link above. Also, > > make sure it is > > set to > > executable > > by typing > > the > > following in a terminal > > window: > > > > $> chmod > > a+x > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > And then > > try again. > > > > -Zeke > > > > > > > Hi > > doug... recon-all dosen't > > working.. > > > > > > If i > > type the recon-all -i~ > > > then, > > error occured... > > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > + > > + > > + > > ++ > > > > > > JPEG > > compressed, decompressing > > > cd > > > > > > /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 > > > > > dcmdjpeg.fs +te > > > > > > > > > > /usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm > > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL >& > > > > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out > > > ERROR: > > 32512, see > > > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out > > for > > > more > > details > > > Linux > > localhost.localdomain > > > > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 > > > 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 > > GNU/Linux > > > > > > > > recon-all -s subj01 exited with > > ERRORS at > > Fri Apr 3 > > 10:39:27 > > PDT 2015 > > > > > > For more > > details, see the log > > file > > > > > > > > > > > > > >/usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log
> > > To > > report a problem, see > > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > + > > + > > + > > +++ > > > > > > I copy > > the libdcmjpeg.so.3.6 and > > paste in > > > > FREESURFER_HOME/lib > > > after > > that type the setenv > > LD_LIBRARY_PATH > > > > $FREESURFER_HOME/lib > > > > > > but.. > > didn't working .. > > > > > > same > > error occured --> > > dcmdjpeg.fs: error > > while loading > > shared > > libraries: > > >...
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Hi A-reum
can you please follow the bug-reporting procedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you
cheers Bruce
On Sun, 18 Oct 2015, A-reum Min wrote:
hello experts. I have a question to you...
I'm doing recon-all stage... but errors showed up (fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve greve@nmr.mgh.harvard.edu: don't use .hdr. When you have a .hdr/.img pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote: hello, expertsI have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001
and then error occured....
ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015
For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Specify something for --seg. It just needs to be a surface overlay of the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com
> > Hello developer~ > > I have some questions to you. > > 1. Does FreeSurfer offer a effect size? if that offer, how can i > use effect size? > > 2. I was wondering about the stats.dat file in stats_table (in > Qdec folder). > > Stats.dat file’s value mean that each area’s average (include > whole vertex) or each > > area’s average (only significant vertex)? > > 3. Can I get whole vertex value or significant vertex value? > Because, I want to > > compare two groups correlation using SPSS. In addition, I want to > compare > > thickness, volume and surface area correlation within the one > group using SPSS. > > 4. I currently use the default cluster size(significant area > threshold is 0mm^2). So, I > > want to control cluster size larger than
default
cluster size. How > can I control the > > cluster size? > > 5. In FreeSurfer manual, GLM and Qdec have a
same
results. But > when I use the > > both(GLM, Qdec) group analysis program results
are
not same. What > is differences > > between two analysis program? How can I get
same
result while GLM > and Qdec? > > 6. How can I get surface area and volume using GLM(group analysis > program)? > > > thanks for your help > > > 2015-07-27 14:28 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>: > > Hello bruce > > I solve this problem(12.png) > > Thank you > > 2015-07-27 13:03 GMT+09:00 dgw <dgwakeman@gmail.com mailto:dgwakeman@gmail.com > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com>>: > > Hi A-reum, > > I think you may be able to get a faster response if you > include some > details about your setup: I would start with the following: > >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> and run bugr. > > hth > D > > On 7/26/15 5:17 PM, A-reum Min wrote: > > Hi, Bruce > > > > When i use a Qdec, this
message(12.png)
show up.. > > How can i solve this problem? > > > > 2015-07-23 22:57 GMT+09:00 Bruce
Fischl
> <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>: > > > > 1. No, each subject has a
different
#. You can map > to fsaverage > > (this is what -qcache does if you specify it for > recon-all), then > > they will have the same #. > > > > 2. What result data do you mean? > > > > 3. Yes, although I'll leave the details to Doug > (since I don't > > remember how his cluster code
works).
> > > > 4. The significance doesn't
depend
on the cluster > size unless you do > > multiple comparison corrections (and even then only > if you do them a > > certain way) > > > > cheers > > Bruce > > > > > > On Thu, 23 Jul 2015, A-reum Min
wrote:
> > > > HELLO developer > > I have some question to you.. > > > > 1. Every patient is given to the same number > of vertex? > > > > 2. When i use a Qdec, How can I
get the
> subject result data? > > > > 3. Could i get the significant
vertex’s
> number, extent of the > > significant area and gray matter
volume?
> > > > 4. Is it significant blue color which how > many connected > > vertex? > > > > > > 2015-05-29 2:03 GMT+09:00 A-reum Min > <naniyaah@gmail.com mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com
> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treat
the
Design > menu exactly.. > > >
---------------------------------------------------------------------------
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
---------------------------------------------------------------------------
> > which one click before analyze? > > > > age range is 12years~24years/ > > all subjects are adolescent. > > and no outlier in age range.. so.. age > (continuous factor) does not > > nasessart? > > > > > > 2015-05-29 1:19 GMT+09:00 A-reum Min > <naniyaah@gmail.com mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com> > > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com
> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treat
the
Design > menu exactly.. > > >
---------------------------------------------------------------------------
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
---------------------------------------------------------------------------
> > which one click before analyze? > > > > > > > > 2015-04-05 21:41 GMT+09:00 Bruce
Fischl
> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>: > > I'm glad it worked out > > Bruce > > On Sun, 5 Apr 2015, A-reum Min
wrote:
> > > > Hello Bruce~ > > You're right.. my PISA dicom
file
> header > > is too short > > so, freesurfer didn't read
it.
> > > > Therefore I use another
subjects
dicom > > file and then freesurfer read
it!
> > > > thank you for u r adavice to
me.
> > > > I really appreciate u > > > > 2015-04-05 7:08 GMT+09:00
Bruce
Fischl > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>: > > Hi A-reum > > > > the problem is that
newer
> versions > > of scanner software
compress
> > dicoms and the version of FS you > > have doesn't know how to
read
> > it. So you need to decompress > them > > before passing them to > > recon-all > > > > cheers > > Bruce > > On Sun, 5 Apr 2015, A-reum Min > > wrote: > > > > Hello developer~ > > > > Can you summarize what the > > problem is? > > ==> > > my problem is recon-all -i > > didn't working... > > so, if i type the recon-all > > -i~then show up theses > > > > > > >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, see > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 GNU/Linux > > > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > > > >
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > then, i click the > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > Are you trying to read > > compressed dicom? > > ==> > > Am i trying to read > > compressed dicom? > > I send my 10071579.dicom(i > > use this) to you, > > using -i, convert the dicom > > file to mgh file. i just > > know that dicom file > > convert to mgz format using > > -i /my data path > > Is it right..?? > > > > > > If so, Can you try running > > dcmdjpeg on it to create > > a new (uncompressed) > > series and give that to > > recon-all? > > ==> (actually, i didn't > > understand your sentence > > means perfectly..) > > zeke > > >
tomeaurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c
> > > > en > > t > > os6_x86_64/dcmdjpeg.fs) > > and then, replace my > > existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs
file.
> > Also, make sure it is set to > > executable by typing > > the following in a > > terminal window: > > $> chmod a+x > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > > > 2015-04-05 2:30 GMT+09:00 > > Bruce Fischl > > > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>: > > Hi A-reum > > > > sorry, I'm coming into > > this late. Can you > > summarize what the > > problem is? Are you > > trying to read compressed > > dicom? If so, can > > you try running > > dcmdjpeg on it to create a
new
> > (uncompressed) > > series and give that > > to recon-all? > > > > cheers > > Bruec > > > > > > > > On Sat, 4 Apr 2015, > > A-reum Min wrote: > > > > Hello > > developers.. > > > > i type the > > recon-all -i~then show up > > theses > > > > > > > > >
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 > > UTC 2014 x86_64 > > x86_64 x86_64 GNU/Linux > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such file
or
> > directory > > > > > > > > >
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > error is occured > > (a little differntly..) > > then, i click > > the > > > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such file
or
> > directory > > > > i'm so sorry..to > > bother you.. > > > > > > > > 2015-04-04 9:21 > > GMT+09:00 A-reum Min > > > > <naniyaah@gmail.com mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: > > hello > > > > i type the > > recon-all -i~ > > then show up > > theses > > >
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > > > ERROR: 32256, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out > > for more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 UTC > > 2014 x86_64 x86_64 x86_64 > > GNU/Linux > > >
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > the error is > > occured (a little > > differntly..) > > then, i click > > the > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, > > show iuo these > > > > sh: > > > >
/usr/local/freesurfer/bin/dcmdjpeg.fs:
> > > > /lib/ld-linux.so.2: bad ELF > > interpreter: No > > such file or directory > > > > plz help me > > 2015-04-04 4:12 > > GMT+09:00 > > > >
<zkaufman@nmr.mgh.harvard.edu
mailto:zkaufman@nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu> > > <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu > <mailto:zkaufman@nmr.mgh.harvard.edu mailto:zkaufman@nmr.mgh.harvard.edu>>>: > > A-reum, > > > > Please > > download the following > > file: > > > > >
ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_
> > > > > > > > > > x86_64/dcmdjpeg.fs > > > > And > > replace your existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > file with > > the > > one from > > the link above. Also, > > make sure it is > > set to > > executable > > by typing > > the > > following in a terminal > > window: > > > > $> chmod > > a+x > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > And then > > try again. > > > > -Zeke > > > > > > > Hi > > doug... recon-all dosen't > > working.. > > > > > > If i > > type the recon-all -i~ > > > then, > > error occured... > > > > > > > >
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > + > > + > > + > > ++ > > > > > > JPEG > > compressed, decompressing > > > cd > > > > > > /usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01 > > > > > dcmdjpeg.fs +te > > > > > > > > > >
/usr/local/freesurfer/subjects/PISA_FSPGR/1/I0071579.dcm
> > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL
&
> > > > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out > > > ERROR: > > 32512, see > > > > > > > > /tmp/root.tmp.decompressed.dcm.kBIYHL.dcmdjpeg.out > > for > > > more > > details > > > Linux > > localhost.localdomain > > > > 2.6.32-504.el6.x86_64 #1 SMP > > Wed Oct 15 > > > 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 > > GNU/Linux > > > > > > > > recon-all -s subj01 exited
with
> > ERRORS at > > Fri Apr 3 > > 10:39:27 > > PDT 2015 > > > > > > For more > > details, see the log > > file > > > > > > > > > > > > > >
/usr/local/freesurfer/subjects/PISA_FSPGR/1/subj01/scripts/recon-all.log
> > > To > > report a problem, see > > > > > > > > > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > >
>++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > + > > + > > + > > +++ > > > > > > I copy > > the libdcmjpeg.so.3.6 and > > paste in > > > > FREESURFER_HOME/lib > > > after > > that type the setenv > > LD_LIBRARY_PATH > > > > $FREESURFER_HOME/lib > > > > > > but.. > > didn't working .. > > > > > > same > > error occured --> > > dcmdjpeg.fs: error > > while loading > > shared > > libraries: > > >
...
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hello experts.
i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... - reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ...
converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/
[areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
can you please follow the bug-reporting procedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you
cheers Bruce
On Sun, 18 Oct 2015, A-reum Min wrote:
hello experts.
I have a question to you...
I'm doing recon-all stage... but errors showed up (fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve greve@nmr.mgh.harvard.edu: don't use .hdr. When you have a .hdr/.img pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote: hello, expertsI have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001
and then error occured....
ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015
For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Specify something for --seg. It just needs to be a surface overlay of the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com> > Hello developer~ > > I have some questions to you. > > 1. Does FreeSurfer offer a effect size? if that offer, how can i > use effect size? > > 2. I was wondering about the stats.dat file in stats_table (in > Qdec folder). > > Stats.dat file’s value mean that each area’s average (include > whole vertex) or each > > area’s average (only significant vertex)? > > 3. Can I get whole vertex value or significant vertex value? > Because, I want to > > compare two groups correlation using SPSS. In addition, I want to > compare > > thickness, volume and surface area correlation within the one > group using SPSS. > > 4. I currently use the default cluster size(significant area > threshold is 0mm^2). So, I > > want to control cluster size larger thandefault
cluster size. How > can I control the > > cluster size? > > 5. In FreeSurfer manual, GLM and Qdec have asame
results. But > when I use the > > both(GLM, Qdec) group analysis program resultsare
not same. What > is differences > > between two analysis program? How can I getsame
result while GLM > and Qdec? > > 6. How can I get surface area and volume using GLM(group analysis > program)? > > > thanks for your help > > > 2015-07-27 14:28 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce > > I solve this problem(12.png) > > Thank you > > 2015-07-27 13:03 GMT+09:00 dgw <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>: > > Hi A-reum, > > I think you may be able to get a faster response if you > include some > details about your setup: I would start with the following: > >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> and run bugr. > > hth > D > > On 7/26/15 5:17 PM, A-reum Min wrote: > > Hi, Bruce > > > > When i use a Qdec, thismessage(12.png)
show up.. > > How can i solve this problem? > > > > 2015-07-23 22:57 GMT+09:00 BruceFischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > > > 1. No, each subject has adifferent
#. You can map > to fsaverage > > (this is what -qcache does if you specify it for > recon-all), then > > they will have the same #. > > > > 2. What result data do you mean? > > > > 3. Yes, although I'll leave the details to Doug > (since I don't > > remember how his cluster codeworks).
> > > > 4. The significance doesn'tdepend
on the cluster > size unless you do > > multiple comparison corrections (and even then only > if you do them a > > certain way) > > > > cheers > > Bruce > > > > > > On Thu, 23 Jul 2015, A-reum Minwrote:
> > > > HELLO developer > > I have some question to you.. > > > > 1. Every patient is given to the same number > of vertex? > > > > 2. When i use a Qdec, How can Iget the
> subject result data? > > > > 3. Could i get the significantvertex’s
> number, extent of the > > significant area and gray mattervolume?
> > > > 4. Is it significant blue color which how > many connected > > vertex? > > > > > > 2015-05-29 2:03 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treatthe
Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > age range is 12years~24years/ > > all subjects are adolescent. > > and no outlier in age range.. so.. age > (continuous factor) does not > > nasessart? > > > > > > 2015-05-29 1:19 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treatthe
Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > > > > > 2015-04-05 21:41 GMT+09:00 BruceFischl
> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > I'm glad it worked out > > Bruce > > On Sun, 5 Apr 2015, A-reum Minwrote:
> > > > Hello Bruce~ > > You're right.. my PISA dicomfile
> header > > is too short > > so, freesurfer didn't readit.
> > > > Therefore I use anothersubjects
dicom > > file and then freesurfer readit!
> > > > thank you for u r adavice tome.
> > > > I really appreciate u > > > > 2015-04-05 7:08 GMT+09:00Bruce
Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > the problem is thatnewer
> versions > > of scanner softwarecompress
> > dicoms and the version of FS you > > have doesn't know how toread
> > it. So you need to decompress > them > > before passing them to > > recon-all > > > > cheers > > Bruce > > On Sun, 5 Apr 2015, A-reum Min > > wrote: > > > > Hello developer~ > > > > Can you summarize what the > > problem is? > > ==> > > my problem is recon-all -i > > didn't working... > > so, if i type the recon-all > > -i~then show up theses > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, see > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 GNU/Linux > > > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > then, i click the > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > Are you trying to read > > compressed dicom? > > ==> > > Am i trying to read > > compressed dicom? > > I send my 10071579.dicom(i > > use this) to you, > > using -i, convert the dicom > > file to mgh file. i just > > know that dicom file > > convert to mgz format using > > -i /my data path > > Is it right..?? > > > > > > If so, Can you try running > > dcmdjpeg on it to create > > a new (uncompressed) > > series and give that to > > recon-all? > > ==> (actually, i didn't > > understand your sentence > > means perfectly..) > > zeke > > >tomeaurl( ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c
> > > > en > > t > > os6_x86_64/dcmdjpeg.fs) > > and then, replace my > > existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fsfile.
> > Also, make sure it is set to > > executable by typing > > the following in a > > terminal window: > > $> chmod a+x > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > > > 2015-04-05 2:30 GMT+09:00 > > Bruce Fischl > > > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > sorry, I'm coming into > > this late. Can you > > summarize what the > > problem is? Are you > > trying to read compressed > > dicom? If so, can > > you try running > > dcmdjpeg on it to create anew
> > (uncompressed) > > series and give that > > to recon-all? > > > > cheers > > Bruec > > > > > > > > On Sat, 4 Apr 2015, > > A-reum Min wrote: > > > > Hello > > developers.. > > > > i type the > > recon-all -i~then show up > > theses > > > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 > > UTC 2014 x86_64 > > x86_64 x86_64 GNU/Linux > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such fileor
> > directory > > > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > error is occured > > (a little differntly..) > > then, i click > > the > > > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such fileor
> > directory > > > > i'm so sorry..to > > bother you.. > > > > > > > > 2015-04-04 9:21 > > GMT+09:00 A-reum Min > > > > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: > > hello > > > > i type the > > recon-all -i~ > > then show up > > theses > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > > > ERROR: 32256, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out > > for more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 UTC > > 2014 x86_64 x86_64 x86_64 > > GNU/Linux > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > the error is > > occured (a little > > differntly..) > > then, i click > > the > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, > > show iuo these > > > > sh: > > > >/usr/local/freesurfer/bin/dcmdjpeg.fs:
> > > > /lib/ld-linux.so.2: bad ELF > > interpreter: No > > such file or directory > > > > plz help me > > 2015-04-04 4:12 > > GMT+09:00 > > > ><zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> > > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>>>: > > A-reum, > > > > Please > > download the following > > file: > > > > >ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_
> > > > > > > > > > x86_64/dcmdjpeg.fs > > > > And > > replace your existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > file with > > the > > one from > > the link above. Also, > > make sure it is > > set to > > executable > > by typing > > the > > following in a terminal > > window: > > > > $> chmod > > a+x > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > And then > > try again. > > > > -Zeke > > > > > > > Hi > > doug... recon-all dosen't > > working.. > > > > > > If i > > type the recon-all -i~
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hello experts.
i have some question to you...
when i enter the recon-all -i /paht~
error showed up.... like below one..
how can i to fix it?
[areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_robust_template --mov /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015
For more details, see the log file /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
2015-10-19 11:05 GMT+09:00 A-reum Min naniyaah@gmail.com:
hello experts.
i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
- voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417)
voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ...
converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/
[areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
can you please follow the bug-reporting procedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you
cheers Bruce
On Sun, 18 Oct 2015, A-reum Min wrote:
hello experts.
I have a question to you...
I'm doing recon-all stage... but errors showed up (fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve greve@nmr.mgh.harvard.edu: don't use .hdr. When you have a .hdr/.img pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote: hello, expertsI have some question.
I want to use analyze format instead of DICOM file.
So, i type this sentence
recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001
and then error occured....
ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015
For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Specify something for --seg. It just needs to be a surface overlay of the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com> > Hello developer~ > > I have some questions to you. > > 1. Does FreeSurfer offer a effect size? if that offer, how can i > use effect size? > > 2. I was wondering about the stats.dat file in stats_table (in > Qdec folder). > > Stats.dat file’s value mean that each area’s average (include > whole vertex) or each > > area’s average (only significant vertex)? > > 3. Can I get whole vertex value or significant vertex value? > Because, I want to > > compare two groups correlation using SPSS. In addition, I want to > compare > > thickness, volume and surface area correlation within the one > group using SPSS. > > 4. I currently use the default cluster size(significant area > threshold is 0mm^2). So, I > > want to control cluster size larger thandefault
cluster size. How > can I control the > > cluster size? > > 5. In FreeSurfer manual, GLM and Qdec have asame
results. But > when I use the > > both(GLM, Qdec) group analysis program resultsare
not same. What > is differences > > between two analysis program? How can I getsame
result while GLM > and Qdec? > > 6. How can I get surface area and volume using GLM(group analysis > program)? > > > thanks for your help > > > 2015-07-27 14:28 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce > > I solve this problem(12.png) > > Thank you > > 2015-07-27 13:03 GMT+09:00 dgw <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>: > > Hi A-reum, > > I think you may be able to get a faster response if you > include some > details about your setup: I would start with the following: > >http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
> and run bugr. > > hth > D > > On 7/26/15 5:17 PM, A-reum Min wrote: > > Hi, Bruce > > > > When i use a Qdec, thismessage(12.png)
show up.. > > How can i solve this problem? > > > > 2015-07-23 22:57 GMT+09:00 BruceFischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > > > 1. No, each subject has adifferent
#. You can map > to fsaverage > > (this is what -qcache does if you specify it for > recon-all), then > > they will have the same #. > > > > 2. What result data do you mean? > > > > 3. Yes, although I'll leave the details to Doug > (since I don't > > remember how his cluster codeworks).
> > > > 4. The significance doesn'tdepend
on the cluster > size unless you do > > multiple comparison corrections (and even then only > if you do them a > > certain way) > > > > cheers > > Bruce > > > > > > On Thu, 23 Jul 2015, A-reum Minwrote:
> > > > HELLO developer > > I have some question to you.. > > > > 1. Every patient is given to the same number > of vertex? > > > > 2. When i use a Qdec, How can Iget the
> subject result data? > > > > 3. Could i get the significantvertex’s
> number, extent of the > > significant area and gray mattervolume?
> > > > 4. Is it significant blue color which how > many connected > > vertex? > > > > > > 2015-05-29 2:03 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treatthe
Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > age range is 12years~24years/ > > all subjects are adolescent. > > and no outlier in age range.. so.. age > (continuous factor) does not > > nasessart? > > > > > > 2015-05-29 1:19 GMT+09:00 A-reum Min > <naniyaah@gmail.com <mailto:naniyaah@gmail.com><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com> > hello developer~ > > reconstruction is well done, so i'm doing on > 'qdec' step.. > > Actually, i don't know how to treatthe
Design > menu exactly.. > > >
> > Discrete(fixed factors) : diagnosis > > continuous (covariate) : age , > Left-Lateral-Ventricle > > >
> > which one click before analyze? > > > > > > > > 2015-04-05 21:41 GMT+09:00 BruceFischl
> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > I'm glad it worked out > > Bruce > > On Sun, 5 Apr 2015, A-reum Minwrote:
> > > > Hello Bruce~ > > You're right.. my PISA dicomfile
> header > > is too short > > so, freesurfer didn't readit.
> > > > Therefore I use anothersubjects
dicom > > file and then freesurfer readit!
> > > > thank you for u r adavice tome.
> > > > I really appreciate u > > > > 2015-04-05 7:08 GMT+09:00Bruce
Fischl > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > the problem is thatnewer
> versions > > of scanner softwarecompress
> > dicoms and the version of FS you > > have doesn't know how toread
> > it. So you need to decompress > them > > before passing them to > > recon-all > > > > cheers > > Bruce > > On Sun, 5 Apr 2015, A-reum Min > > wrote: > > > > Hello developer~ > > > > Can you summarize what the > > problem is? > > ==> > > my problem is recon-all -i > > didn't working... > > so, if i type the recon-all > > -i~then show up theses > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, see > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 04:27:16 > > UTC 2014 x86_64 x86_64 > > x86_64 GNU/Linux > > > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > then, i click the > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > dcmdjpeg.fs: error while > > loading shared libraries: > > libijg8.so.3.6: cannot > > open shared object file: No > > such file or directory > > > > Are you trying to read > > compressed dicom? > > ==> > > Am i trying to read > > compressed dicom? > > I send my 10071579.dicom(i > > use this) to you, > > using -i, convert the dicom > > file to mgh file. i just > > know that dicom file > > convert to mgz format using > > -i /my data path > > Is it right..?? > > > > > > If so, Can you try running > > dcmdjpeg on it to create > > a new (uncompressed) > > series and give that to > > recon-all? > > ==> (actually, i didn't > > understand your sentence > > means perfectly..) > > zeke > > >tomeaurl( ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/c
> > > > en > > t > > os6_x86_64/dcmdjpeg.fs) > > and then, replace my > > existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fsfile.
> > Also, make sure it is set to > > executable by typing > > the following in a > > terminal window: > > $> chmod a+x > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > > > 2015-04-05 2:30 GMT+09:00 > > Bruce Fischl > > > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>: > > Hi A-reum > > > > sorry, I'm coming into > > this late. Can you > > summarize what the > > problem is? Are you > > trying to read compressed > > dicom? If so, can > > you try running > > dcmdjpeg on it to create anew
> > (uncompressed) > > series and give that > > to recon-all? > > > > cheers > > Bruec > > > > > > > > On Sat, 4 Apr 2015, > > A-reum Min wrote: > > > > Hello > > developers.. > > > > i type the > > recon-all -i~then show up > > theses > > > > > > > > >++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > ERROR: 32512, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out > > for > > more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 > > UTC 2014 x86_64 > > x86_64 x86_64 GNU/Linux > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such fileor
> > directory > > > > > > > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > error is occured > > (a little differntly..) > > then, i click > > the > > > > > > root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, > > show > > up > > these > > > > dcmdjpeg.fs: > > error while loading shared > > libraries: > > libijg8.so.3.6: > > cannot > > open shared > > object file: No such fileor
> > directory > > > > i'm so sorry..to > > bother you.. > > > > > > > > 2015-04-04 9:21 > > GMT+09:00 A-reum Min > > > > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>><mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: > > hello > > > > i type the > > recon-all -i~ > > then show up > > theses > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > > > ERROR: 32256, > > see > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out > > for more details > > Linux > > localhost.localdomain > > 2.6.32-504.el6.x86_64 #1 > > SMP Wed Oct 15 > > 04:27:16 UTC > > 2014 x86_64 x86_64 x86_64 > > GNU/Linux > > >+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
> > > > > > > > +++++++ > > the error is > > occured (a little > > differntly..) > > then, i click > > the > > > > > > /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, > > show iuo these > > > > sh: > > > >/usr/local/freesurfer/bin/dcmdjpeg.fs:
> > > > /lib/ld-linux.so.2: bad ELF > > interpreter: No > > such file or directory > > > > plz help me > > 2015-04-04 4:12 > > GMT+09:00 > > > ><zkaufman@nmr.mgh.harvard.edu
<mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>> > > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu> > <mailto:zkaufman@nmr.mgh.harvard.edu <mailto:zkaufman@nmr.mgh.harvard.edu>>>>: > > A-reum, > > > > Please > > download the following > > file: > > > > >ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6_
> > > > > > > > > > x86_64/dcmdjpeg.fs > > > > And > > replace your existing > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > file with > > the > > one from > > the link above. Also, > > make sure it is > > set to > > executable > > by typing > > the > > following in a terminal > > window: > > > > $> chmod > > a+x > > > > $FREESURFER_HOME/bin/dcmdjpeg.fs > > > > And then > > try again. > > > > -Zeke > > > > > > > Hi > > doug... recon-all dosen't > > working.. > > > > > > If i > > type the recon-all -i~
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are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it.
cheers Bruce
On Thu, 5 Nov 2015, A-reum Min wrote:
hello experts. i have some question to you...
when i enter the recon-all -i /paht~
error showed up.... like below one..
how can i to fix it?
[areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_robust_template --mov /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015
For more details, see the log file /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
2015-10-19 11:05 GMT+09:00 A-reum Min naniyaah@gmail.com: hello experts. i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>-------------------------------------------------------------------------- - >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >>> mailto:naniyaah@gmail.com> >>> > > <mailto:naniyaah@gmail.com >>> mailto:naniyaah@gmail.com >>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu>>>: >>> > > Hi A-reum >>> > > >>> > > the problem is that newer >>> > versions >>> > > of scanner software compress >>> > > dicoms and the version of FS you >>> > > have doesn't know how to read >>> > > it. So you need to >>> decompress >>> > them >>> > > before passing them to >>> > > recon-all >>> > > >>> > > cheers >>> > > Bruce >>> > > On Sun, 5 Apr 2015, >>> A-reum Min >>> > > wrote: >>> > > >>> > > Hello developer~ >>> > > >>> > > Can you summarize what the >>> > > problem is? >>> > > ==> >>> > > my problem is recon-all -i >>> > > didn't working... >>> > > so, if i type the recon-all >>> > > -i~then show up theses >>> > > >>> > > >>> > > >>> > >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> > > ERROR: 32512, see >>> > > >>> > > >>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >>> > > for >>> > > more details >>> > > Linux localhost.localdomain >>> > > 2.6.32-504.el6.x86_64 #1 >>> > > SMP Wed Oct 15 04:27:16 >>> > > UTC 2014 x86_64 x86_64 >>> > > x86_64 GNU/Linux >>> > > >>> > > dcmdjpeg.fs: error while >>> > > loading shared libraries: >>> > > libijg8.so.3.6: cannot >>> > > open shared object file: No >>> > > such file or directory >>> > > >>> > > >>> > > >>> > >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> > > >>> > > then, i click the >>> > > >>> > > >>> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >>> > > show >>> > > up >>> > > these >>> > > dcmdjpeg.fs: error while >>> > > loading shared libraries: >>> > > libijg8.so.3.6: cannot >>> > > open shared object file: No >>> > > such file or directory >>> > > >>> > > Are you trying to read >>> > > compressed dicom? >>> > > ==> >>> > > Am i trying to read >>> > > compressed dicom? >>> > > I send my 10071579.dicom(i >>> > > use this) to you, >>> > > using -i, convert the dicom >>> > > file to mgh file. i just >>> > > know that dicom file >>> > > convert to mgz format using >>> > > -i /my data path >>> > > Is it right..?? >>> > > >>> > > >>> > > If so, Can you try running >>> > > dcmdjpeg on it to create >>> > > a new (uncompressed) >>> > > series and give that to >>> > > recon-all? >>> > > ==> (actually, i didn't >>> > > understand your sentence >>> > > means perfectly..) >>> > > zeke >>> > > >>> > >>> tomeaurl(ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binarie s/c >>> > > >>> > > en >>> > > t >>> > > os6_x86_64/dcmdjpeg.fs) >>> > > and then, replace my >>> > > existing >>> > > >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs file. >>> > > Also, make sure it is set to >>> > > executable by typing >>> > > the following in a >>> > > terminal window: >>> > > $> chmod a+x >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >>> > > >>> > > >>> > > 2015-04-05 2:30 GMT+09:00 >>> > > Bruce Fischl >>> > > >>> > > <fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> mailto:fischl@nmr.mgh.harvard.edu>>>: >>> > > Hi A-reum >>> > > >>> > > sorry, I'm coming into >>> > > this late. Can you >>> > > summarize what the >>> > > problem is? Are you >>> > > trying to read compressed >>> > > dicom? If so, can >>> > > you try running >>> > > dcmdjpeg on it to create a new >>> > > (uncompressed) >>> > > series and give that >>> > > to recon-all? >>> > > >>> > > cheers >>> > > Bruec >>> > > >>> > > >>> > > >>> > > On Sat, 4 Apr 2015, >>> > > A-reum Min wrote: >>> > > >>> > > Hello >>> > > developers.. >>> > > >>> > > i type the >>> > > recon-all -i~then show up >>> > > theses >>> > > >>> > > >>> > > >>> > > >>> > >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> > > ERROR: 32512, >>> > > see >>> > > >>> > > >>> > > >>> /tmp/root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out >>> > > for >>> > > more details >>> > > Linux >>> > > localhost.localdomain >>> > > 2.6.32-504.el6.x86_64 #1 >>> > > SMP Wed Oct 15 >>> > > 04:27:16 >>> > > UTC 2014 x86_64 >>> > > x86_64 x86_64 GNU/Linux >>> > > >>> > > dcmdjpeg.fs: >>> > > error while loading shared >>> > > libraries: >>> > > libijg8.so.3.6: >>> > > cannot >>> > > open shared >>> > > object file: No such file or >>> > > directory >>> > > >>> > > >>> > > >>> > > >>> > >>> +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ >>> > > >>> > > error is occured >>> > > (a little differntly..) >>> > > then, i click >>> > > the >>> > > >>> > > >>> > > >>> root.tmp.decompressed.dcm.55srMV.dcmdjpeg.out, >>> > > show >>> > > up >>> > > these >>> > > >>> > > dcmdjpeg.fs: >>> > > error while loading shared >>> > > libraries: >>> > > libijg8.so.3.6: >>> > > cannot >>> > > open shared >>> > > object file: No such file or >>> > > directory >>> > > >>> > > i'm so sorry..to >>> > > bother you.. >>> > > >>> > > >>> > > >>> > > 2015-04-04 9:21 >>> > > GMT+09:00 A-reum Min >>> > > >>> > > <naniyaah@gmail.com >>> mailto:naniyaah@gmail.com >>> > <mailto:naniyaah@gmail.com >>> mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> mailto:naniyaah@gmail.com >>> > <mailto:naniyaah@gmail.com >>> mailto:naniyaah@gmail.com>>>: >>> > > hello >>> > > >>> > > i type the >>> > > recon-all -i~ >>> > > then show up >>> > > theses >>> > > >>> > >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + >>> > > >>> > > >>> > > >>> > > +++++++ >>> > > >>> > > ERROR: 32256, >>> > > see >>> > > >>> > > >>> > > >>> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out >>> > > for more details >>> > > Linux >>> > > localhost.localdomain >>> > > 2.6.32-504.el6.x86_64 #1 >>> > > SMP Wed Oct 15 >>> > > 04:27:16 UTC >>> > > 2014 x86_64 x86_64 x86_64 >>> > > GNU/Linux >>> > > >>> > >>> ++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ + >>> > > >>> > > >>> > > >>> > > +++++++ >>> > > the error is >>> > > occured (a little >>> > > differntly..) >>> > > then, i click >>> > > the >>> > > >>> > > >>> > > >>> /tmp/root.tmp.decompressed.dcm.XhbJG3.dcmdjpeg.out, >>> > > show iuo these >>> > > >>> > > sh: >>> > > >>> > > /usr/local/freesurfer/bin/dcmdjpeg.fs: >>> > > >>> > > /lib/ld-linux.so.2: bad ELF >>> > > interpreter: No >>> > > such file or directory >>> > > >>> > > plz help me >>> > > 2015-04-04 4:12 >>> > > GMT+09:00 >>> > > >>> > > <zkaufman@nmr.mgh.harvard.edu >>> mailto:zkaufman@nmr.mgh.harvard.edu >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >>> mailto:zkaufman@nmr.mgh.harvard.edu> >>> > > <mailto:zkaufman@nmr.mgh.harvard.edu >>> mailto:zkaufman@nmr.mgh.harvard.edu >>> > <mailto:zkaufman@nmr.mgh.harvard.edu >>> mailto:zkaufman@nmr.mgh.harvard.edu>>>: >>> > > A-reum, >>> > > >>> > > Please >>> > > download the following >>> > > file: >>> > > >>> > > >>> > >>> ftp://surfer.nmr.mgh.harvard.edu//pub/dist/freesurfer/dev_binaries/centos6 _ >>> > > >>> > > >>> > > >>> > > >>> > > x86_64/dcmdjpeg.fs >>> > > >>> > > And >>> > > replace your existing >>> > > >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >>> > > file with >>> > > the >>> > > one from >>> > > the link above. Also, >>> > > make sure it is >>> > > set to >>> > > executable >>> > > by typing >>> > > the >>> > > following in a terminal >>> > > window: >>> > > >>> > > $> chmod >>> > > a+x >>> > > >>> > > $FREESURFER_HOME/bin/dcmdjpeg.fs >>> > > >>> > > And then >>> > > try again. >>> > > >>> > > -Zeke >>> > > >>> > >
> > > Hi > > doug...
recon-all dosen't
> > working.. > > > > > > If i > > type the
recon-all -i~
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Hello bruce!
I solve the problem for your answer.
And.. i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
How can i to do?
2015-11-05 22:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it.
cheers Bruce
On Thu, 5 Nov 2015, A-reum Min wrote:
hello experts.
i have some question to you...
when i enter the recon-all -i /paht~
error showed up.... like below one..
how can i to fix it?
[areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_robust_template --mov /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015
For more details, see the log file /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
2015-10-19 11:05 GMT+09:00 A-reum Min naniyaah@gmail.com: hello experts. i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
- voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512,
- voxels. -- Reslicing using cubic bspline
MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ...
converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/
[areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>
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Hello experts!
i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
2015-11-08 20:44 GMT+09:00 A-reum Min naniyaah@gmail.com:
Hello bruce!
I solve the problem for your answer.
And.. i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
How can i to do?
2015-11-05 22:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it.
cheers Bruce
On Thu, 5 Nov 2015, A-reum Min wrote:
hello experts.
i have some question to you...
when i enter the recon-all -i /paht~
error showed up.... like below one..
how can i to fix it?
[areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002
mri_robust_template --mov /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015
For more details, see the log file /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
2015-10-19 11:05 GMT+09:00 A-reum Min naniyaah@gmail.com: hello experts. i have a question to you..
i'm doing recon-all stage, but errors show up like this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1
Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz )
-- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512,
- voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512,
- voxels. -- Reslicing using cubic bspline
MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 )
- running loop to estimate saturation parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ...
converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/
[areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015
For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu>
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Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote:
Hello experts!
i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
Hello bruce! I solve the problem for your answer. And.. i have some question to you.. How can i control the cluster size? My cluster threshold is 1. then, too many blue regions (as shown fig.1). so, i want to control cluster threshold 1--> cluster threshold 5. How can i to do? 2015-11-05 22:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it. cheers Bruce On Thu, 5 Nov 2015, A-reum Min wrote: hello experts. i have some question to you... when i enter the recon-all -i /paht~ error showed up.... like below one.. how can i to fix it? [areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... #-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_robust_template --mov /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz ) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015 For more details, see the log file /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up like this ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt --subsample 200 --lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta / $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and output results --subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... MRItoBSpline degree 3 reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT iteratively! i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... - reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... n reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz ) Badly placed ()'s. e [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubic bspline a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [areum@localhost 14]# [areum@localhost 14]# For more details, see the log file /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/ mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT iteratively! --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to init TP! --fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... reading: Command not found. [areum@localhost 14]# converting source '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 ( /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz ) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubic bspline --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identical images?) Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we are to be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>> >>> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>> -------------------------------------------------------------------------- - >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Hello experts!
I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote:
Hello experts!
i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
Hello bruce! I solve the problem for your answer. And.. i have some question to you.. How can i control the cluster size? My cluster threshold is 1. then, too many blue regions (as shown fig.1). so, i want to control cluster threshold 1--> cluster threshold 5. How can i to do? 2015-11-05 22:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it. cheers Bruce On Thu, 5 Nov 2015, A-reum Min wrote: hello experts. i have some question to you... when i enter the recon-all -i /paht~ error showed up.... like below one.. how can i to fix it? [areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
#-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_robust_template --mov/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
--average 1 --template/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015 For more details, see the log file/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up like this ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/ $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_template.cpp,v1.37.2.2
2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SATiteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to initTP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
- reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) Badly placed ()'s. e [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimatesaturation
parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [areum@localhost 14]# [areum@localhost 14]# For more details, see the log file/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/ mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/sub reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. [areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 for template computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SATiteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to initTP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensity scaling! --iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we areto
be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>> >>> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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hello experts! my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min naniyaah@gmail.com:
Hello experts!
I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote:
Hello experts!
i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
Hello bruce! I solve the problem for your answer. And.. i have some question to you.. How can i control the cluster size? My cluster threshold is 1. then, too many blue regions (as shown fig.1). so, i want to control cluster threshold 1--> cluster threshold 5. How can i to do? 2015-11-05 22:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it. cheers Bruce On Thu, 5 Nov 2015, A-reum Min wrote: hello experts. i have some question to you... when i enter the recon-all -i /paht~ error showed up.... like below one.. how can i to fix it? [areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
#-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_robust_template --mov/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
--average 1 --template/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015 For more details, see the log file/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up like this ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz --satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/ $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_template.cpp,v1.37.2.2
2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 fortemplate
computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SATiteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to initTP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensityscaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
- reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) Badly placed ()'s. e [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimatesaturation
parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT2015
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [areum@localhost 14]# [areum@localhost 14]# For more details, see the log file/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/ mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from/usr/local/freesurfer/sub
reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command notfound.
[areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-frame in Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 fortemplate
computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SATiteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything to initTP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensityscaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identical image Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reporting procedures in: https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if we areto
be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>> >>> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
<mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
<mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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hello experts! my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. --> 3T imaging protocol completed True ver. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-24 23:32 GMT+09:00 A-reum Min naniyaah@gmail.com:
hello experts! my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min naniyaah@gmail.com:
Hello experts!
I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote:
Hello experts!
i have some question to you..
How can i control the cluster size?
My cluster threshold is 1.
then, too many blue regions (as shown fig.1).
so, i want to control cluster threshold 1--> cluster threshold 5.
2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
Hello bruce! I solve the problem for your answer. And.. i have some question to you.. How can i control the cluster size? My cluster threshold is 1. then, too many blue regions (as shown fig.1). so, i want to control cluster threshold 1--> cluster threshold 5. How can i to do? 2015-11-05 22:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm images from *different* series or from the *same* series? If they are in the same series than that explains what is happening. You should only give recon-all a single file from any one acquisition - it will figure out the rest of the files that are part of it. cheers Bruce On Thu, 5 Nov 2015, A-reum Min wrote: hello experts. i have some question to you... when i enter the recon-all -i /paht~ error showed up.... like below one.. how can i to fix it? [areum@localhost 0165766_1]# recon-all -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm -all -s sub002 Subject Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Current Stamp: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /usr/local/freesurfer/subjects/OSA/0165766_1 Actual FREESURFER_HOME /usr/local/freesurfer Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
mri_convert /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... Starting DICOMRead2() dcmfile = /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
#-------------------------------------------- #@# MotionCor Thu Nov 5 02:27:17 PST 2015 Found 2 runs/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
Checking for (invalid) multi-frame inputs... Checking for (invalid) multi-frame inputs... #----------------------------------------------- /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 mri_robust_template --mov/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
--average 1 --template/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
$Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub002 exited with ERRORS at Thu Nov 5 02:37:57 PST 2015 For more details, see the log file/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up like this ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/ $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template computation. --template: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no iterations)! --iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and outputresults
--subsample: Will subsample if size is larger than 200 on all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation parameter: Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_template.cpp,v1.37.2.2
2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1 fortemplate
computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SATiteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything toinit TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensityscaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample if size is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA transforms --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
- reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# MultiRegistration::initializing Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) Badly placed ()'s. e [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using cubicbspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimatesaturation
parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT2015
Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:33 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting [areum@localhost 14]# [areum@localhost 14]# For more details, see the log file/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# recon-all -i /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i /usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/ mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 dicom files in series. Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... Starting DICOMRead2() dcmfile =/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from/usr/local/freesurfer/sub
reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking for dicoms Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found. [areum@localhost 14]# #---------------------------- #----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command notfound.
[areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid) multi-frame inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid) multi-framein
Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014: Permission denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1 fortemplate
computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SATiteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as target for initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything toinit TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only first template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing intensityscaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform intensity scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init] ========================= TP 2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 ( /usr/l Too many ('s. [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0.4688, 0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original : (0.4688, 0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using cubicbspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to estimate saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimage
Too many ('s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0 (identicalimages?)
Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32 Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited with ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct 17 08:35:53 PDT 2015 For more details, see the log file To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reporting proceduresin:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting also, don't include a snapshot of text - cutting and pasting the actual text in is far more useful, but in addition we need a lot of other information if weare to
be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errors showed up (fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a .hdr/.img pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead of DICOM file. So, i type this sentence recon-all -i /usr/local/freesurfer/subjects/test_han/I0071579.hdr -i /usr/local/freesurfer/subjects/test_han/I0071579.img -all -s han001 and then error occured.... ERROR: cannot determine file type for /usr/local/freesurfer/subjects/test_han/I0071579.hdr Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s han001 exited with ERRORS at Wed Sep 16 06:35:02 PDT 2015 For more details, see the log file/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It just needs to be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Min wrote: > Hello doug > > i enter the ' mri_segstats --i y.mgh --vox 33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must specify a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just put the vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min wrote: >> Hello developer, >> >> I have some question to you. >> >> How can i get the significant vertices value using Qdec result? >> >> When i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error ouccured --> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats --i y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error occured --> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00 Douglas Greve >> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum Min wrote: >>> Hello developers >>> >>> I have some question to you. >>> >>> 1.In fig.png, how many vertices were composed of cluster at >>> least? >> I'm not sure what you mean. it does not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by the clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the threshold when specifying "--cache >> threshold sign" to mri_glmfit-sim >>> >>> 4. What is the difference between two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue and the other is the >> cluster-forming thershold >>> >>> 5. What is the exactly mean two words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00 Douglas N Greve >>> <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: >>> >>> >>> >>> On 08/10/2015 10:06 PM, A-reum Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I have some question to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a group analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s value mean that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole vertex value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to compare >>> > >>> > thickness, volume and surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a given vertex with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects where the value is the data from the >>> given (0-based) >>> vertex no. y.mgh is the input to mri_glmfit >>> > >>> > 4. I currently use the default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you mean. >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec) group analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless you tell us the specifics of what >>> you did >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and volume are outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>
>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions to you. >>> > >>> > 1. Does FreeSurfer offer a effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering about the stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value mean that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole vertex value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and surface area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the default cluster >>> size(significant area >>> > threshold is 0mm^2). So, I >>> > >>> > want to control cluster size larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer manual, GLM and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group analysis program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get surface area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28 GMT+09:00 A-reum Min >>> <naniyaah@gmail.com <mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>
>>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03 GMT+09:00 dgw >>> <dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>> >>> > <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com> >>> <mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com>>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
>>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
>>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
<mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com <mailto:naniyaah@gmail.com> >>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
>>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>> >>> > > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
>>> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>> >>> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>
<mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> >>> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
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Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce
On Thu, 24 Dec 2015, A-reum Min wrote:
hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min naniyaah@gmail.com: Hello experts! I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.commailto:naniyaah@gmail.com>: hello experts. i have a question to you..
i'm doing recon-all stage, but errors show up like
this
ects/OSA/14/subj014/mri/orig/002.mgz --average 1
--template
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale --iscaleout
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/ $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $
--mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for template
computation.
--template: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (no
iterations)!
--iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling and
output results
--subsample: Will subsample if size is larger than
200 on
all axes! --lta: Will output LTA transforms reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3
MultiRegistration::initializing Xforms (init 1 ,
maxres 0
, iterate 5 , epsit 0.01 ) :
[init] ========================= TP 2 to TP 1 ============================== Register TP 2 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
)
-- Original : (0.4688, 0.4688, 0.800001) mm
size
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm
size and
(512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mm
size
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mm
size and
(512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3
- Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturation
parameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]#
[areum@localhost 14]# $Id:
mri_robust_template.cpp,v 1.37.2.2
2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1
for template
computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SAT
iteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as
target for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything
to init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only
first
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing
intensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform
intensity
scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsample
if size
is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTA
transforms
--lta:: Too many arguments. [areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
- reading: Command not found. [areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n reading: Command not found. [areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ...
converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]#
MultiRegistration::initializing
Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init]
========================= TP
2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) Badly placed ()'s. e [areum@localhost 14]# to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original :
(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:
(0.4688,
0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using
cubic bspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original :
(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:
(0.4688,
0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing using
cubic bspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to
estimate saturation
parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16
UTC 2014
x86_64 x86_64 x86_64 GNU/Linux
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited
with
ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17
07:50:15 PDT 2015
Linux localhost.localdomain 2.6.32-504.el6.x86_64
#1 SMP
Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct
17
08:35:33 PDT 2015
For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see the
log file
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]#
recon-all -i
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm
-i
/usr/local/
[areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014:
Permission
denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/
mri_convert: missing output volume name
type mri_convert -u for usage
[areum@localhost 14]# $Id: mri_convert.c,v
1.179.2.7
2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm...
reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking
for dicoms
Found: Command not found. [areum@localhost 14]# Found 244 dicom files in
series.
Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00,
flip
angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc
mri_convert
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16
mreuter
Exp $ reading from
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm...
Starting DICOMRead2() dcmfile =
/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v
1.179.2.7
2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from
/usr/local/freesurfer/sub
reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checking
for dicoms
Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00,
flip
angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found. [areum@localhost 14]#
#----------------------------
#----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 17
08:09:23
PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Command
not found.
[areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid)
multi-frame
inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid)
multi-frame in
Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------:
Command
not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014:
Permission
denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1
for template
computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SAT
iteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 as
target for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everything
to init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output only
first
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableing
intensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will perform
intensity
scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init]
========================= TP
2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 (
/usr/l
Too many ('s. [areum@localhost 14]# to TP 1 (
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original :
(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:
(0.4688,
0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing using
cubic bspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original :
(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing using
cubic bspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop to
estimate
saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical image
Too many ('s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0
(identical images?)
Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain
2.6.32
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exited
with
ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64
#1 SMP
Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
recon-all -s subj014 exited with ERRORS at Sat Oct
17
08:35:53 PDT 2015
For more details, see the log file To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do?
plz help me..
2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>: Hi A-reum
can you please follow the bug-reporting
procedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text -
cutting and
pasting the actual text in is far more
useful, but in
addition we need a lot of other information
if we are to
be able to help you
cheers Bruce
On Sun, 18 Oct 2015, A-reum Min wrote:
hello experts. I have a question to you...
I'm doing recon-all stage... but errors
showed up
(fig.1)
how can i to do?
plz, help me
2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>: don't use .hdr. When you have a
.hdr/.img
pair, just use the .img file.
On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question.
I want to use analyze format instead of
DICOM file.
So, i type this sentence
recon-all -i
/usr/local/freesurfer/subjects/test_han/I0071579.hdr
-i
/usr/local/freesurfer/subjects/test_han/I0071579.img
-all -s han001
and then error occured....
ERROR: cannot determine file type for
/usr/local/freesurfer/subjects/test_han/I0071579.hdr
Linux localhost.localdomain
2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64
GNU/Linux
recon-all -s han001 exited with ERRORS at
Wed Sep 16
06:35:02 PDT 2015
For more details, see the log file
/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, see
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format?
2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>: Specify something for --seg. It just
needs to
be a surface overlay of the same size as the input.
On 08/27/2015 01:49 AM, A-reum Min
wrote:
> Hello doug > > i enter the ' mri_segstats --i y.mgh
--vox
33 0 0 --avgwf out.dat' > then, error occured --> ERROR: must
specify
a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 Douglas
Greve
<greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>: > > don't use "vertexno", just put
the
vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Min
wrote:
>> Hello developer, >> >> I have some question to you. >> >> How can i get the significant
vertices
value using Qdec result? >> >> When i enter the 'mri_segstats
--i
y.mgh --vox vertexno 33 0 0 >> --avgwf out.dat', then error
ouccured
--> ERROR : Option out.dat >> unknown. >> >> So, i enter the 'mri_segstats
--i y.mgh
--vox vertexno 33 0 0 >> --avgwf out.dat', then error
occured
--> ERROR : Option 0 unkown. >> >> How can i fix it? >> >> >> >> >> >> >> >> 2015-08-25 23:41 GMT+09:00
Douglas
Greve >> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>: >> >> >> >> On 8/25/15 9:35 AM, A-reum
Min
wrote: >>> Hello developers >>> >>> I have some question to
you.
>>> >>> 1.In fig.png, how many
vertices
were composed of cluster at >>> least? >> I'm not sure what you mean.
it does
not look like there are >> any clusters there >>> >>> 2. How to change Area Threshold(fig.png)? >> The area is controlled by
the
clusterwise threshold (--cwp) >> to mri_glmfit-sim >>> >>> 3. How to change CSD thresh(fig.png)? >> That is controlled by the
threshold
when specifying "--cache >> threshold sign" to
mri_glmfit-sim
>>> >>> 4. What is the difference
between
two words(Area Threshold, >>> CSD thresh)? >> One is the cluster-pvalue
and the
other is the >> cluster-forming thershold >>> >>> 5. What is the exactly
mean two
words(Area Threshold, CSD >>> thresh)? >> See above >> >>> >>> Thank you >>> >>> 2015-08-12 23:23 GMT+09:00
Douglas
N Greve >>> <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu>>: >>> >>> >>> >>> On 08/10/2015 10:06
PM, A-reum
Min wrote: >>> > HI expert ! >>> > >>> > My name is Areum. I
have
some question to you. >>> > >>> > 1. Does FreeSurfer
offer a
effect size? if that offer, >>> how can i use >>> > effect size? >>> > >>> If you're doing a
group
analysis, you can compute >>> fscalc glmdir/contrast/gamma.mgh div glmdir/rstd.mgh -o >>> glmdir/contrast/effectsize.mgh >>> > >>> > 2. I was wondering
about the
stats.dat file in >>> stats_table (in Qdec >>> > folder). >>> > >>> > Stats.dat file’s
value mean
that each area’s average >>> (include whole >>> > vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> what stats.dat? if subject/stats/lh.aparc.stats, then >>> the area is the >>> total area for the ROI >>> > >>> > 3. Can I get whole
vertex
value or significant vertex >>> value? Because, >>> > I want to >>> > >>> > compare two groups correlation using SPSS. In >>> addition, I want to
compare
>>> > >>> > thickness, volume
and
surface area correlation within >>> the one group >>> > using SPSS. >>> > >>> You can extract a
given vertex
with >>> mri_segstats --i y.mgh --crs vertexno 0 0 --avgwf >>> vertexno.dat >>> vertexno.dat will be a text file with number of rows >>> equalt to thge >>> number of subjects
where the
value is the data from the >>> given (0-based) >>> vertex no. y.mgh is
the input
to mri_glmfit >>> > >>> > 4. I currently use
the
default cluster >>> size(significant area threshold >>> > is 0mm^2). So, I >>> > >>> > want to control
cluster size
larger than default >>> cluster size. How can >>> > I control the >>> > >>> > cluster size? >>> > >>> I don't know what you
mean.
>>> > >>> > 5. In FreeSurfer
manual, GLM
and Qdec have a same >>> results. But when I >>> > use the >>> > >>> > both(GLM, Qdec)
group
analysis program results are not >>> same. What is >>> > differences >>> > >>> > between two analysis program? How can I get same >>> result while GLM and >>> > Qdec? >>> > >>> No way to know unless
you tell
us the specifics of what >>> you did >>> > >>> > 6. How can I get
surface
area and volume using >>> GLM(group analysis >>> > program)? >>> > >>> surface area and
volume are
outputs of recon-all, not glm >>> > >>> > >>> > plz reply to me >>> > >>> > >>> > 2015-08-10 21:35
GMT+09:00
A-reum Min >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> > <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello developer~ >>> > >>> > I have some questions
to you.
>>> > >>> > 1. Does FreeSurfer
offer a
effect size? if that >>> offer, how can i >>> > use effect size? >>> > >>> > 2. I was wondering
about the
stats.dat file in >>> stats_table (in >>> > Qdec folder). >>> > >>> > Stats.dat file’s value
mean
that each area’s >>> average (include >>> > whole vertex) or each >>> > >>> > area’s average (only significant vertex)? >>> > >>> > 3. Can I get whole
vertex
value or significant >>> vertex value? >>> > Because, I want to >>> > >>> > compare two groups
correlation
using SPSS. In >>> addition, I want to >>> > compare >>> > >>> > thickness, volume and
surface
area correlation >>> within the one >>> > group using SPSS. >>> > >>> > 4. I currently use the
default
cluster >>> size(significant area >>> > threshold is 0mm^2). So,
I
>>> > >>> > want to control
cluster size
larger than default >>> cluster size. How >>> > can I control the >>> > >>> > cluster size? >>> > >>> > 5. In FreeSurfer
manual, GLM
and Qdec have a same >>> results. But >>> > when I use the >>> > >>> > both(GLM, Qdec) group
analysis
program results are >>> not same. What >>> > is differences >>> > >>> > between two analysis
program?
How can I get same >>> result while GLM >>> > and Qdec? >>> > >>> > 6. How can I get
surface area
and volume using >>> GLM(group analysis >>> > program)? >>> > >>> > >>> > thanks for your help >>> > >>> > >>> > 2015-07-27 14:28
GMT+09:00
A-reum Min >>> <naniyaah@gmail.com mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com
>>> >
<mailto:naniyaah@gmail.com
mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>: >>> > >>> > Hello bruce >>> > >>> > I solve this problem(12.png) >>> > >>> > Thank you >>> > >>> > 2015-07-27 13:03
GMT+09:00
dgw >>> <dgwakeman@gmail.com mailto:dgwakeman@gmail.com <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com> >>> > <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com >>> <mailto:dgwakeman@gmail.com mailto:dgwakeman@gmail.com>>>: >>> > >>> > Hi A-reum, >>> > >>> > I think you may be able to get a faster >>> response if you >>> > include some >>> > details about your setup: I would start >>> with the following: >>> > >>> >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
>>> > and run bugr. >>> > >>> > hth >>> > D >>> > >>> > On 7/26/15 5:17 PM, A-reum Min wrote: >>> > > Hi, Bruce >>> > > >>> > > When i use a Qdec, this message(12.png) >>> show up.. >>> > > How can i solve this problem? >>> > > >>> > > 2015-07-23 22:57 GMT+09:00 Bruce Fischl >>> > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > >>> > > 1. No, each subject has a different >>> #. You can map >>> > to fsaverage >>> > > (this is what -qcache does if you >>> specify it for >>> > recon-all), then >>> > > they will have the same #. >>> > > >>> > > 2. What result data do you mean? >>> > > >>> > > 3. Yes, although I'll leave the >>> details to Doug >>> > (since I don't >>> > > remember how his cluster code works). >>> > > >>> > > 4. The significance doesn't depend >>> on the cluster >>> > size unless you do >>> > > multiple comparison corrections (and >>> even then only >>> > if you do them a >>> > > certain way) >>> > > >>> > > cheers >>> > > Bruce >>> > > >>> > > >>> > > On Thu, 23 Jul 2015, A-reum Min wrote: >>> > > >>> > > HELLO developer >>> > > I have some question to you.. >>> > > >>> > > 1. Every patient is given to the >>> same number >>> > of vertex? >>> > > >>> > > 2. When i use a Qdec, How can I get the >>> > subject result data? >>> > > >>> > > 3. Could i get the significant vertex’s >>> > number, extent of the >>> > > significant area and gray matter volume? >>> > > >>> > > 4. Is it significant blue color >>> which how >>> > many connected >>> > > vertex? >>> > > >>> > > >>> > > 2015-05-29 2:03 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > age range is 12years~24years/ >>> > > all subjects are adolescent. >>> > > and no outlier in age range.. >>> so.. age >>> > (continuous factor) does not >>> > > nasessart? >>> > > >>> > > >>> > > 2015-05-29 1:19 GMT+09:00 A-reum Min >>> > <naniyaah@gmail.com mailto:naniyaah@gmail.com >>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>> >>> > > <mailto:naniyaah@gmail.com
>>> <mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com> >>> > <mailto:naniyaah@gmail.com
<mailto:naniyaah@gmail.com mailto:naniyaah@gmail.com>>>>: >>> > > hello developer~ >>> > > reconstruction is well done, so i'm >>> doing on >>> > 'qdec' step.. >>> > > Actually, i don't know how to treat the >>> Design >>> > menu exactly.. >>> > > >>> > >>>
- >>> > > Discrete(fixed factors) : diagnosis >>> > > continuous (covariate) : age , >>> > Left-Lateral-Ventricle >>> > > >>> > >>>
- >>> > > which one click before analyze? >>> > > >>> > > >>> > > >>> > > 2015-04-05 21:41 GMT+09:00 Bruce Fischl >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>> <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu>>>>: >>> > > I'm glad it worked out >>> > > Bruce >>> > > On Sun, 5 Apr 2015, A-reum Min wrote: >>> > > >>> > > Hello Bruce~ >>> > > You're right.. my PISA dicom file >>> > header >>> > > is too short >>> > > so, freesurfer didn't read it. >>> > > >>> > > Therefore I use another subjects >>> dicom >>> > > file and then freesurfer read it! >>> > > >>> > > thank you for u r adavice to me. >>> > > >>> > > I really appreciate u >>> > > >>> > > 2015-04-05 7:08 GMT+09:00 Bruce >>> Fischl >>> > > <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu> >>> > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>> >>> > > <mailto:fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu >>>
<mailto:fischl@nmr.mgh.harvard.edu
mailto:fischl@nmr.mgh.harvard.edu>
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hello experts! my name is areum. i have some question to you. i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce
On Thu, 24 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-11-10 7:49 GMT+09:00 A-reum Min naniyaah@gmail.com: Hello experts! I have some question to you..
I don't need to show up so small blue regions(fig.1 blue region)
How can i control these?
2015-11-10 7:41 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate.
On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/00 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.tx t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com
<mailto:naniyaah@gmail.com>>: hello experts. i have a question to you.. i'm doing recon-all stage, but errors show up likethis
ects/OSA/14/subj014/mri/orig/002.mgz --average 1--template
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
--satit --inittp 1 --fixtp --noit --iscale --iscaleout/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt
--subsample 200 --lta/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta
/ $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 19:59:06 mreuter Exp $ --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. Total: 2 input volumes --average: Using method 1 for templatecomputation.
--template: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --satit: Will estimate SAT iteratively! --inittp: Using TP 1 as target for initialization --fixtp: Will map everything to init TP! --noit: Will output only first template (noiterations)!
--iscale: Enableing intensity scaling! --iscaleout: Will perform intensity scaling andoutput results
--subsample: Will subsample if size is larger than200 on
all axes! --lta: Will output LTA transforms reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... MRItoBSpline degree 3 reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... MRItoBSpline degree 3 MultiRegistration::initializing Xforms (init 1 ,maxres 0
, iterate 5 , epsit 0.01 ) : [init] ========================= TP 2 to TP 1 ============================== Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) -- Original : (0.4688, 0.4688, 0.800001) mmsize
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mmsize and
(512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 -- Original : (0.4688, 0.4688, 0.800001) mmsize
and (512, 512, 244) voxels. -- Resampled: (0.4688, 0.4688, 0.4688) mmsize and
(512, 512, 417) voxels. -- Reslicing using cubic bspline MRItoBSpline degree 3 - Max Resolution used: 3 -- gpS ( 64 , 64 , 52 ) -- gpT ( 64 , 64 , 52 ) - running loop to estimate saturationparameter:
Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Sigma too small: 0 (identical images?) Killed [areum@localhost 14]# [areum@localhost 14]# $Id:mri_robust_template.cpp,v 1.37.2.2
2012/10/10 19:59:06 mreuter Exp $ c Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
as movable/source volume. --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. b [areum@localhost 14]# --average: Using method 1for template
computation. --average:: Too many arguments. [areum@localhost 14]# --template: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz
as template output volume. --template:: Too many arguments. [areum@localhost 14]# --satit: Will estimate SATiteratively!
i --satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 astarget for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everythingto init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output onlyfirst
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableingintensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will performintensity
scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsample: Will subsampleif size
is larger than 200 on all axes! --subsample:: Too many arguments. [areum@localhost 14]# --lta: Will output LTAtransforms
--lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
- reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... b converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 r MRItoBSpline: Command not found. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'...
n reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 p MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]#MultiRegistration::initializing
Xforms (init 1 , maxres 0 , iterate 5 , epsit 0.01 ) : / Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# [init]========================= TP
2 to TP 1 ============================== a [init]: No match. [areum@localhost 14]# Register TP 2 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
) Badly placed ()'s. e [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) n Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original :(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:(0.4688,
0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing usingcubic bspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 T MRItoBSpline: Command not found. [areum@localhost 14]# -- Original :(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:(0.4688,
0.4688, 0.4688) mm size and (512, 512, 417) voxels. Badly placed (. [areum@localhost 14]# -- Reslicing usingcubic bspline
a --: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 u MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 i -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop toestimate saturation
parameter: l -: Command not found. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. 4 [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Killed . Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16UTC 2014
x86_64 x86_64 x86_64 GNU/Linux Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exitedwith
ERRORS at Sat Oct 17 07:50:15 PDT 2015 a ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 1707:50:15 PDT 2015
Linux localhost.localdomain 2.6.32-504.el6.x86_64#1 SMP
Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct17
08:35:33 PDT 2015 For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
[areum@localhost 14]# [areum@localhost 14]# For more details, see thelog file
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log
For: Command not found. [areum@localhost 14]# To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
e To: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]#recon-all -i
/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm-i
/usr/local/ [areum@localhost: Command not found. [areum@localhost 14]# Subject Stamp: freesurfer-Linux-centos6_x86_6 i Subject: Command not found. [areum@localhost 14]# Current Stamp: freesurfer-Linux-centos6_x8 2 Current: Command not found. [areum@localhost 14]# INFO: SUBJEC INFO:: Too many arguments. [areum@localhost 14]# Actual FREESURFER_HOME /usr/local/freesurfer 8 Actual: Command not found. [areum@localhost 14]# Linux localhost.l s Linux: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 g /usr/local/freesurfer/subjects/OSA/14/subj014:Permission
denied. [areum@localhost 14]# [areum@localhost 14]# mri_convert /u mri_convert /u mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/ mri_convert /usr/local/freesurfer/subjects/ mri_convert: missing output volume name type mri_convert -u for usage [areum@localhost 14]# $Id: mri_convert.c,v1.179.2.7
2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from/usr/local/freesurfer/subjects/OSA/14/I0000001.dcm...
reading: Command not found. [areum@localhost 14]# Startin Startin: Command not found. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checkingfor dicoms
Found: Command not found. [areum@localhost 14]# Found 244 dicom files inseries.
Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00,flip
angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to /usr/local/freesurfer/subjects/OSA/14/subj014/ writing: Command not found. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm/usr/loc
mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/loc mri_convert: can't determine type of output volume [areum@localhost 14]# [areum@localhost 14]# mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
mri_convert/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16mreuter
Exp $ reading from/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm...
Starting DICOMRead2() dcmfile =/usr/local/freesurfer/subjects/OSA/14/I0000002.dcm
dcmdir = /usr/local/freesurfer/subjects/OSA/14 Ref Series No = 3 Found 247 files, checking for dicoms Found 244 dicom files in series. First Sorting Computing Slice Direction Vs: -0.8 0 0 Vs: -1 0 0 Second Sorting Counting frames nframes = 1 nslices = 244 ndcmfiles = 244 PE Dir = ROW (dicom read) TransferSyntaxUID: --1.2.840.10008.1.2.1-- Loading pixel data TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 i_ras = (0, -1, 0) j_ras = (0, 0, -1) k_ras = (1, -0, 0) writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
[areum@localhost 14]# $Id: mri_convert.c,v1.179.2.7
2012/09/05 21:55:16 mreuter Exp $ Bad : modifier in $ ( ). [areum@localhost 14]# reading from/usr/local/freesurfer/sub
reading: Command not found. [areum@localhost 14]# Starting DICOMRead2() Badly placed ()'s. [areum@localhost 14]# dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm dcmfile: Command not found. [areum@localhost 14]# dcmdir = /usr/local/freesurfer/subjects/OSA/14 dcmdir: Command not found. [areum@localhost 14]# Ref Series No = 3 Ref: Command not found. [areum@localhost 14]# Found 247 files, checkingfor dicoms
Found: Command not found. [areum@localhost 14]# Found 244 di Found: Command not found. [areum@localhost 14]# First Sorting First: Command not found. [areum@localhost 14]# Computing Slice Direction Computing: Command not found. [areum@localhost 14]# Vs: -0.8 0 0 Vs:: Too many arguments. [areum@localhost 14]# Vs: -1 0 0 Vs:: Too many arguments. [areum@localhost 14]# Second Sorting Second: Command not found. [areum@localhost 14]# Counting frames Counting: Command not found. [areum@localhost 14]# nframes = 1 nframes: Command not found. [areum@localhost 14]# nslices = 244 nslices: Command not found. [areum@localhost 14]# ndcmfiles = 244 ndcmfiles: Command not found. [areum@localhost 14]# PE Dir = ROW (dicom read) Badly placed ()'s. [areum@localhost 14]# TransferSyntaxUID: --1.2.840.10008.1.2.1-- TransferSyntaxUID:: Too many arguments. [areum@localhost 14]# Loading pixel data Loading: Command not found. [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00,flip
angle=12.00 TR=7.70,: Command not found. [areum@localhost 14]# i_ras = (0, -1, 0) Badly placed ()'s. [areum@localhost 14]# j_ras = (0, 0, -1) Badly placed ()'s. [areum@localhost 14]# k_ras = (1, -0, 0) Badly placed ()'s. [areum@localhost 14]# writing to/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz...
writing: Command not found. [areum@localhost 14]##----------------------------
#----------------------------: Command not found. [areum@localhost 14]# #@# MotionCor Sat Oct 1708:09:23
PDT 2015 #@#: Command not found. [areum@localhost 14]# Found 2 runs Found: Command not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/sub /usr/local/freesurfer/subjects/OSA/14/sub: Commandnot found.
[areum@localhost 14]# /usr/local/freesurfer /usr/local/freesurfer: Permission denied. [areum@localhost 14]# Checking for (invalid)multi-frame
inputs... Badly placed ()'s. [areum@localhost 14]# Checking for (invalid)multi-frame in
Badly placed ()'s. [areum@localhost 14]# #----------------------------------------------- #-----------------------------------------------:Command
not found. [areum@localhost 14]# /usr/local/freesurfer/subjects/OSA/14/subj014 /usr/local/freesurfer/subjects/OSA/14/subj014:Permission
denied. [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# [areum@localhost 14]# $Id: mri_robust_temp Bad : modifier in $ ( ). [areum@localhost 14]# [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
as movable/ --mov:: Too many arguments. [areum@localhost 14]# --mov: Using/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz
a --mov:: Too many arguments. [areum@localhost 14]# Total: 2 input volumes Total:: Too many arguments. [areum@localhost 14]# --average: Using method 1for template
computation. --average:: Too many arguments. [areum@localhost 14]# --template --template: Command not found. [areum@localhost 14]# --satit: Will estimate SATiteratively!
--satit:: Too many arguments. [areum@localhost 14]# --inittp: Using TP 1 astarget for
initialization --inittp:: Too many arguments. [areum@localhost 14]# --fixtp: Will map everythingto init TP!
--fixtp:: Too many arguments. [areum@localhost 14]# --noit: Will output onlyfirst
template (no iterations)! Badly placed ()'s. [areum@localhost 14]# --iscale: Enableingintensity scaling!
--iscale:: Too many arguments. [areum@localhost 14]# --iscaleout: Will performintensity
scaling and output results --iscaleout:: Too many arguments. [areum@localhost 14]# --subsa --subsa: Command not found. [areum@localhost 14]# --lta: Will output LT --lta:: Too many arguments. [areum@localhost 14]# reading source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'...
reading: Command not found. [areum@localhost 14]# converting source'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'
to bspline ... converting: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# rea rea: Command not found. [areum@localhost 14]# converting source '/u Unmatched '. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# Multi Multi: Command not found. [areum@localhost 14]# [areum@localhost 14]# [init]========================= TP
2 to TP 1 ============================== [init]: No match. [areum@localhost 14]# Register TP 2 (/usr/l
Too many ('s. [areum@localhost 14]# to TP 1 (/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz
) Badly placed ()'s. [areum@localhost 14]# [areum@localhost 14]# -- Original :(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled:(0.4688,
0.4688, 0.4688) mm size and (512, 512, 4 Too many ('s. [areum@localhost 14]# -- Reslicing usingcubic bspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# -- Original :(0.4688,
0.4688, 0.800001) mm size and (512, 512, 244) voxels. Badly placed (. [areum@localhost 14]# -- Resampled: (0. Too many ('s. [areum@localhost 14]# -- Reslicing usingcubic bspline
--: Command not found. [areum@localhost 14]# MRItoBSpline degree 3 MRItoBSpline: Command not found. [areum@localhost 14]# [areum@localhost 14]# - Max Resolution used: 3 -: Command not found. [areum@localhost 14]# -- gpS ( 64 , 64 , Too many ('s. [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) Badly placed ()'s. [areum@localhost 14]# - running loop toestimate
saturation pa -: Command not found. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0 Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical image
Too many ('s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Sigma too small: Sigma: Command not found. [areum@localhost 14]# Sigma too small: 0(identical images?)
Badly placed ()'s. [areum@localhost 14]# Si Si: Command not found. [areum@localhost 14]# Killed Killed: Command not found. [areum@localhost 14]# Linux localhost.localdomain2.6.32
Linux: Command not found. [areum@localhost 14]# [areum@localhost 14]# recon-all -s subj014 exitedwith
ERRORS at Sat Oct 17 08 ERROR: Flag exited unrecognized. -s subj014 exited with ERRORS at Sat Oct 17 08 Linux localhost.localdomain 2.6.32-504.el6.x86_64#1 SMP
Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux recon-all -s subj014 exited with ERRORS at Sat Oct17
08:35:53 PDT 2015 For more details, see the log file To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
how can i to do? plz help me.. 2015-10-18 0:11 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum can you please follow the bug-reportingprocedures in:
https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
also, don't include a snapshot of text -cutting and
pasting the actual text in is far moreuseful, but in
addition we need a lot of other informationif we are to
be able to help you cheers Bruce On Sun, 18 Oct 2015, A-reum Min wrote: hello experts. I have a question to you... I'm doing recon-all stage... but errorsshowed up
(fig.1) how can i to do? plz, help me 2015-09-16 23:56 GMT+09:00 Douglas Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: don't use .hdr. When you have a.hdr/.img
pair, just use the .img file. On 9/16/15 10:51 AM, A-reum Min wrote: hello, experts I have some question. I want to use analyze format instead ofDICOM file.
So, i type this sentence recon-all -i/usr/local/freesurfer/subjects/test_han/I0071579.hdr
-i/usr/local/freesurfer/subjects/test_han/I0071579.img
-all -s han001 and then error occured.... ERROR: cannot determine file type for/usr/local/freesurfer/subjects/test_han/I0071579.hdr
Linux localhost.localdomain2.6.32-504.el6.x86_64 #1
SMP Wed Oct 15 04:27:16 UTC 2014 x86_64 x86_64 x86_64GNU/Linux
recon-all -s han001 exited with ERRORS atWed Sep 16
06:35:02 PDT 2015 For more details, see the log file/usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log
To report a problem, seehttp://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
How can i to do using analyze format? 2015-08-27 23:55 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Specify something for --seg. It justneeds to
be a surface overlay of the same size as the input. On 08/27/2015 01:49 AM, A-reum Minwrote:
> Hello doug > > i enter the ' mri_segstats --i y.mgh--vox
33 0 0 --avgwf out.dat' > then, error occured --> ERROR: mustspecify
a segmentation volume > > > 2015-08-27 12:50 GMT+09:00 DouglasGreve
<greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> > <mailto:greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>>: > > don't use "vertexno", just putthe
vertex number, eg, --vox 33 0 0 > > > On 8/26/15 9:22 PM, A-reum Minwrote:
>> Hello developer, >> >> I have some question to you. >> >> How can i get the significant
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Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all)
cheers Bruce
On Tue, 29 Dec 2015, A-reum Min wrote:
hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file > /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > g > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# mri_convert /u > mri_convert /u > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/ > mri_convert /usr/local/freesurfer/subjects/ > > mri_convert: missing output volume name > > type mri_convert -u for usage > > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm... > reading: Command not found. > [areum@localhost 14]# Startin > Startin: Command not found. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 dicom files in series. > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/ > writing: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm /usr/loc > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/loc > mri_convert: can't determine type of output volume > [areum@localhost 14]# > [areum@localhost 14]# mri_convert > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > mri_convert /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm... > Starting DICOMRead2() > dcmfile = /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/14 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > [areum@localhost 14]# $Id: mri_convert.c,v 1.179.2.7 > 2012/09/05 > 21:55:16 mreuter Exp $ > Bad : modifier in $ ( ). > [areum@localhost 14]# reading from /usr/local/freesurfer/sub > reading: Command not found. > [areum@localhost 14]# Starting DICOMRead2() > Badly placed ()'s. > [areum@localhost 14]# dcmfile = > /usr/local/freesurfer/subjects/OSA/14/I0000002.dcm > dcmfile: Command not found. > [areum@localhost 14]# dcmdir = > /usr/local/freesurfer/subjects/OSA/14 > dcmdir: Command not found. > [areum@localhost 14]# Ref Series No = 3 > Ref: Command not found. > [areum@localhost 14]# Found 247 files, checking for dicoms > Found: Command not found. > [areum@localhost 14]# Found 244 di > Found: Command not found. > [areum@localhost 14]# First Sorting > First: Command not found. > [areum@localhost 14]# Computing Slice Direction > Computing: Command not found. > [areum@localhost 14]# Vs: -0.8 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Vs: -1 0 0 > Vs:: Too many arguments. > [areum@localhost 14]# Second Sorting > Second: Command not found. > [areum@localhost 14]# Counting frames > Counting: Command not found. > [areum@localhost 14]# nframes = 1 > nframes: Command not found. > [areum@localhost 14]# nslices = 244 > nslices: Command not found. > [areum@localhost 14]# ndcmfiles = 244 > ndcmfiles: Command not found. > [areum@localhost 14]# PE Dir = ROW (dicom read) > Badly placed ()'s. > [areum@localhost 14]# TransferSyntaxUID: > --1.2.840.10008.1.2.1-- > TransferSyntaxUID:: Too many arguments. > [areum@localhost 14]# Loading pixel data > Loading: Command not found. > [areum@localhost 14]# TR=7.70, TE=3.37, TI=400.00, flip > angle=12.00 > TR=7.70,: Command not found. > [areum@localhost 14]# i_ras = (0, -1, 0) > Badly placed ()'s. > [areum@localhost 14]# j_ras = (0, 0, -1) > Badly placed ()'s. > [areum@localhost 14]# k_ras = (1, -0, 0) > Badly placed ()'s. > [areum@localhost 14]# writing to > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz... > writing: Command not found. > [areum@localhost 14]# #---------------------------- > #----------------------------: Command not found. > [areum@localhost 14]# #@# MotionCor Sat Oct 17 08:09:23 > PDT 2015 > #@#: Command not found. > [areum@localhost 14]# Found 2 runs > Found: Command not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/sub > /usr/local/freesurfer/subjects/OSA/14/sub: Command not found. > [areum@localhost 14]# /usr/local/freesurfer > /usr/local/freesurfer: Permission denied. > [areum@localhost 14]# Checking for (invalid) multi-frame > inputs... > Badly placed ()'s. > [areum@localhost 14]# Checking for (invalid) multi-frame in > Badly placed ()'s. > [areum@localhost 14]# > #----------------------------------------------- > #-----------------------------------------------: Command > not found. > [areum@localhost 14]# > /usr/local/freesurfer/subjects/OSA/14/subj014 > /usr/local/freesurfer/subjects/OSA/14/subj014: Permission > denied. > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# > [areum@localhost 14]# $Id: mri_robust_temp > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/ > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > a > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template > --template: Command not found. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsa > --subsa: Command not found. > [areum@localhost 14]# --lta: Will output LT > --lta:: Too many arguments. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# rea > rea: Command not found. > [areum@localhost 14]# converting source '/u > Unmatched '. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# Multi > Multi: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > [init]: No match. > [areum@localhost 14]# Register TP 2 ( /usr/l > Too many ('s. > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 4 > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0. > Too many ('s. > [areum@localhost 14]# -- Reslicing using cubic bspline > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , > Too many ('s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate > saturation pa > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical image > Too many ('s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: > Sigma: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Si > Si: Command not found. > [areum@localhost 14]# Killed > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain 2.6.32 > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 08 > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 08 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:53 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > > > > > > how can i to do? > > plz help me.. > > 2015-10-18 0:11 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu > <mailto:fischl@nmr.mgh.harvard.edu>>: > Hi A-reum > > can you please follow the bug-reporting procedures in: > > https://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > also, don't include a snapshot of text - cutting and > pasting the actual text in is far more useful, but in > addition we need a lot of other information if we are to > be able to help you > > cheers > Bruce > > On Sun, 18 Oct 2015, A-reum Min wrote: > > hello experts. > I have a question to you... > > I'm doing recon-all stage... but errors showed up > (fig.1) > > how can i to do? > > plz, help me > > > 2015-09-16 23:56 GMT+09:00 Douglas Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > don't use .hdr. When you have a .hdr/.img > pair, just use the .img file. > > On 9/16/15 10:51 AM, A-reum Min wrote: > hello, experts > I have some question. > > I want to use analyze format instead of DICOM file. > > So, i type this sentence > > recon-all -i > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > -i > /usr/local/freesurfer/subjects/test_han/I0071579.img > -all -s han001 > > > and then error occured.... > > ERROR: cannot determine file type for > /usr/local/freesurfer/subjects/test_han/I0071579.hdr > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 > SMP Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s han001 exited with ERRORS at Wed Sep 16 > 06:35:02 PDT 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/test_han/han001/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > How can i to do using analyze format? > > > 2015-08-27 23:55 GMT+09:00 Douglas N Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>: > Specify something for --seg. It just needs to > be a surface > overlay of > the same size as the input. > > On 08/27/2015 01:49 AM, A-reum Min wrote: > > Hello doug > > > > i enter the ' mri_segstats --i y.mgh --vox > 33 0 0 --avgwf > out.dat' > > then, error occured --> ERROR: must specify > a segmentation > volume > > > > > > 2015-08-27 12:50 GMT+09:00 Douglas Greve > <greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu> > > <mailto:greve@nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>>>: > > > > don't use "vertexno", just put the > vertex number, eg, > --vox 33 0 0 > > > > > > On 8/26/15 9:22 PM, A-reum Min wrote: > >> Hello developer, > >> > >> I have some question to you. > >> > >> How can i get the significant _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
1) Why isn't the same number of total vertices? is it related rain size?
2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all)
cheers Bruce
On Tue, 29 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout >/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# >
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Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
1) Why isn't the same number of total vertices? is it related brain size?
2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-16 23:39 GMT+09:00 A-reum Min naniyaah@gmail.com:
Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
Why isn't the same number of total vertices? is it related rain size?
How can i extract the number of total vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all)
cheers Bruce
On Tue, 29 Dec 2015, A-reum Min wrote:
hello experts!my name is areum.
i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me
2015-12-25 2:16 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale.t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout >/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# >
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-- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n esthekr@nate.comaniyaah@gmail.com
Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer).
cheers Bruce
On Sat, 16 Jan 2016, A-reum Min wrote:
Hello expert. I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
Why isn't the same number of total vertices? is it related rain size?
How can i extract the number of total vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/ 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale. t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > [areum@localhost 14]# > > [areum@localhost 14]# $Id: mri_robust_template.cpp,v 1.37.2.2 > 2012/10/10 19:59:06 mreuter Exp $ > c > Bad : modifier in $ ( ). > [areum@localhost 14]# > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > --mov:: Too many arguments. > [areum@localhost 14]# Total: 2 input volumes > Total:: Too many arguments. > b > [areum@localhost 14]# --average: Using method 1 for template > computation. > --average:: Too many arguments. > [areum@localhost 14]# --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --template:: Too many arguments. > [areum@localhost 14]# --satit: Will estimate SAT iteratively! > i > --satit:: Too many arguments. > [areum@localhost 14]# --inittp: Using TP 1 as target for > initialization > --inittp:: Too many arguments. > [areum@localhost 14]# --fixtp: Will map everything to init TP! > --fixtp:: Too many arguments. > [areum@localhost 14]# --noit: Will output only first > template (no > iterations)! > Badly placed ()'s. > [areum@localhost 14]# --iscale: Enableing intensity scaling! > --iscale:: Too many arguments. > [areum@localhost 14]# --iscaleout: Will perform intensity > scaling and > output results > --iscaleout:: Too many arguments. > [areum@localhost 14]# --subsample: Will subsample if size > is larger > than 200 on all axes! > --subsample:: Too many arguments. > [areum@localhost 14]# --lta: Will output LTA transforms > --lta:: Too many arguments. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > - > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > b > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > r > MRItoBSpline: Command not found. > [areum@localhost 14]# reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > n > reading: Command not found. > [areum@localhost 14]# converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > > converting: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > p > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# MultiRegistration::initializing > Xforms (init 1 , > maxres 0 , iterate 5 , epsit 0.01 ) : > / > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# [init] ========================= TP > 2 to TP 1 > ============================== > a > [init]: No match. > [areum@localhost 14]# Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > Badly placed ()'s. > e > [areum@localhost 14]# to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > n > Badly placed ()'s. > [areum@localhost 14]# > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > T > MRItoBSpline: Command not found. > [areum@localhost 14]# -- Original : (0.4688, > 0.4688, 0.800001) > mm size and (512, 512, 244) voxels. > Badly placed (. > [areum@localhost 14]# -- Resampled: (0.4688, > 0.4688, 0.4688) mm > size and (512, 512, 417) voxels. > Badly placed (. > [areum@localhost 14]# -- Reslicing using cubic bspline > a > --: Command not found. > [areum@localhost 14]# MRItoBSpline degree 3 > u > MRItoBSpline: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# - Max Resolution used: 3 > i > -: Command not found. > [areum@localhost 14]# -- gpS ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# -- gpT ( 64 , 64 , 52 ) > Badly placed ()'s. > [areum@localhost 14]# - running loop to estimate saturation > parameter: > l > -: Command not found. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > 4 > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Sigma too small: 0 (identical images?) > Badly placed ()'s. > [areum@localhost 14]# Killed > . > Killed: Command not found. > [areum@localhost 14]# Linux localhost.localdomain > 2.6.32-504.el6.x86_64 #1 SMP Wed Oct 15 04:27:16 UTC 2014 > x86_64 > x86_64 x86_64 GNU/Linux > > Linux: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# recon-all -s subj014 exited with > ERRORS at Sat > Oct 17 07:50:15 PDT 2015 > a > ERROR: Flag exited unrecognized. > -s subj014 exited with ERRORS at Sat Oct 17 07:50:15 PDT 2015 > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 > 04:27:16 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s subj014 exited with ERRORS at Sat Oct 17 > 08:35:33 PDT > 2015 > > For more details, see the log file > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > [areum@localhost 14]# > [areum@localhost 14]# For more details, see the log file > /usr/local/freesurfer/subjects/OSA/14/subj014/scripts/recon-all.log > > For: Command not found. > [areum@localhost 14]# To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > e > To: Command not found. > [areum@localhost 14]# > [areum@localhost 14]# [areum@localhost 14]# recon-all -i > /usr/local/freesurfer/subjects/OSA/14/I0000001.dcm -i > /usr/local/ > > [areum@localhost: Command not found. > [areum@localhost 14]# Subject Stamp: > freesurfer-Linux-centos6_x86_6 > i > Subject: Command not found. > [areum@localhost 14]# Current Stamp: > freesurfer-Linux-centos6_x8 > 2 > Current: Command not found. > [areum@localhost 14]# INFO: SUBJEC > INFO:: Too many arguments. > [areum@localhost 14]# Actual FREESURFER_HOME > /usr/local/freesurfer > 8 > Actual: Command not found. > [areum@localhost 14]# Linux localhost.l > s > Linux: Command not found. > [areum@localhost 14]# > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. 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Areum Min Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : naniyaah@gmail.com
Thank you for u r answer.
I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer).
cheers Bruce
On Sat, 16 Jan 2016, A-reum Min wrote:
Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
Why isn't the same number of total vertices? is it related rain size?
How can i extract the number of total vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... >
#-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/ 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale. t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout >/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hello experts
i have some question to you
What method do you use when measuring the cortical thickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?)
plz answer me.
2016-01-17 0:53 GMT+09:00 A-reum Min naniyaah@gmail.com:
Thank you for u r answer.
I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer).
cheers Bruce
On Sat, 16 Jan 2016, A-reum Min wrote:
Hello expert.
I'm Areum.
I have some question to you.
A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices.(176416) -experiment 1.
And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed.
Each group has the same number of vertices(169548) -experiment 2.
Why isn't the same number of total vertices? is it related rain size?
How can i extract the number of total vertices(ex.#1 vertex : cortical
thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-07 3:52 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... >
#-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/ 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale. t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see >
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout >/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( >
/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels.
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n esthekr@nate.comaniyaah@gmail.com
Hi A-reum
we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing.
cheers Bruce
On Fri, 5 Feb 2016, A-reum Min wrote:
hello experts
i have some question to you
What method do you use when measuring the cortical thickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?)
plz answer me.
2016-01-17 0:53 GMT+09:00 A-reum Min naniyaah@gmail.com: Thank you for u r answer. I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig / 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale . t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, 244) > voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, 417) > voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > > - Max Resolution used: 3 > -- gpS ( 64 , 64 , 52 ) > -- gpT ( 64 , 64 , 52 ) > - running loop to estimate saturation parameter: > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Sigma too small: 0 (identical images?) > Killed > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > > recon-all -s sub002 exited with ERRORS at Thu Nov 5 > 02:37:57 PST 2015 > > For more details, see the log file > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/scripts/recon-all.log > To report a problem, see > http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > > 2015-10-19 11:05 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > hello experts. > i have a question to you.. > > i'm doing recon-all stage, but errors show up like this > > > > > ects/OSA/14/subj014/mri/orig/002.mgz --average 1 --template > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale --iscaleout > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001-iscale.txt > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002-iscale.txt > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.lta > > / > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter > Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 > , epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/002.mgz > ) > to TP 1 ( > /usr/local/freesurfer/subjects/OSA/14/subj014/mri/orig/001.mgz > ) > > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels. > -- Reslicing using cubic bspline > MRItoBSpline degree 3 > -- Original : (0.4688, 0.4688, 0.800001) mm size > and (512, 512, > 244) voxels. > -- Resampled: (0.4688, 0.4688, 0.4688) mm size and > (512, 512, > 417) voxels.
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Areum Min Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : naniyaah@gmail.com
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Areum Min Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : naniyaah@gmail.com
hello experts
i have some question to you
What is the meaning about cortical thickness alteration (increase or decrease)
a few days ago i read these sentences
Deviations from these patterns can be used as diagnostic indicators for brain disorders http://en.citizendium.org/wiki/Brain_disorder: While Alzheimer's disease http://en.citizendium.org/wiki/Alzheimer%27s_disease, even very early on, is characterized by pronounced cortical thinning[4] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4 , Williams syndrome http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1 patients exhibit an increase in cortical thickness of about 5-10% in some regions [5] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5, and lissencephalic http://en.citizendium.org/wiki/Lissencephalic patients show drastic thickening, up to several centimetres in occipital regions[6] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6. from wiki
i wonder increased or reduced cortex depended on disorder?
plz answer me
2016-02-06 0:27 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing.
cheers Bruce
On Fri, 5 Feb 2016, A-reum Min wrote:
hello experts
i have some question to you
What method do you use when measuring the cortical thickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?)
plz answer me.
2016-01-17 0:53 GMT+09:00 A-reum Min naniyaah@gmail.com: Thank you for u r answer. I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... >
#-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig / 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale . t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min naniyaah@gmail.com:
hello experts
i have some question to you
What is the meaning about cortical thickness alteration (increase or decrease)
a few days ago i read these sentences
Deviations from these patterns can be used as diagnostic indicators for brain disorders http://en.citizendium.org/wiki/Brain_disorder: While Alzheimer's disease http://en.citizendium.org/wiki/Alzheimer%27s_disease, even very early on, is characterized by pronounced cortical thinning[4] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4 , Williams syndrome http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1 patients exhibit an increase in cortical thickness of about 5-10% in some regions [5] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5, and lissencephalic http://en.citizendium.org/wiki/Lissencephalic patients show drastic thickening, up to several centimetres in occipital regions[6] http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6. from wiki
i wonder increased or reduced cortex depended on disorder?
plz answer me
2016-02-06 0:27 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi A-reum
we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing.
cheers Bruce
On Fri, 5 Feb 2016, A-reum Min wrote:
hello experts
i have some question to you
What method do you use when measuring the cortical thickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?)
plz answer me.
2016-01-17 0:53 GMT+09:00 A-reum Min naniyaah@gmail.com: Thank you for u r answer. I have some question to you.
i compared two groups(patients VS control)
How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex).
plz answer me.
Thank you.
2016-01-17 0:22 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Areum
every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from >
/usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... >
#-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... >
#----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig / 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale . t x t > --subsample 200 --lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >
/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source >
'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( >
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
-- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n esthekr@nate.comaniyaah@gmail.com
usually if the thickness is 0 that means that the vertex is not part of cortex, typically because it is on the "medial wall" (adjacent to ventricle) or in the hippocampus or some other non-neocortical structure
On Fri, 4 Mar 2016, A-reum Min wrote:
hello experts i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min naniyaah@gmail.com: hello experts i have some question to you
What is the meaning about cortical thickness alteration (increase or decrease)
a few days ago i read these sentences
Deviations from these patterns can be used as diagnostic indicators for brain disorders: While Alzheimer's disease, even very early on, is characterized by pronounced cortical thinning[4], Williams syndrome patients exhibit an increase in cortical thickness of about 5-10% in some regions [5], and lissencephalic patients show drastic thickening, up to several centimetres in occipital regions[6]. from wiki
i wonder increased or reduced cortex depended on disorder?
plz answer me
2016-02-06 0:27 GMT+09:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi A-reum
we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the cortical thickness? (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com > <mailto:naniyaah@gmail.com>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/ori g / 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscal e . t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 >============================== > Register TP 2 ( >
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Areum Min Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : naniyaah@gmail.com
for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning^[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4> , Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1> patients exhibit an increase in cortical thickness of about 5-10% in some regions ^[5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5> , and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions^[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6> . from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the cortical thickness? (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into the fsaverage space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz... > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz... > #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig / 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale . t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta > > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz > as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz > as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz > as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz' > to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'... > converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz' > to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <mailto:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
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hi experts
i have some problem using qdec
when i enter the qdec and then 'Generate Stats Data Tables'
show up these sentences
asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 dep_17 dep_18 dep_19 dep_20 dep_21 dep_22 SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep Parsing the .stats files ERROR: The stats file /usr/local/freesurfer/subjects/HCP_sleep/con_12/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
and show up error box(fig1.jpg)
how can i to do.. plz help me.
my data information is
1 diagnosis discrete 2 1 Control 2 Deprivation 2 age continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 28.167 3.280
Number of subjects: 66 Number of factors: 2 (1 discrete, 1 continuous) Number of classes: 2 Number of regressors: 4
rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 -1 0 0)
2016-03-05 0:36 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning^[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4
, Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&r... patients
exhibit an increase in cortical thickness of about 5-10% in some regions ^[5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5
, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions^[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6
. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the cortical thickness? (ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into thefsaverage
space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
> #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> --average 1 --template >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> --satit > --inittp 1 --fixtp --noit --iscale >--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig
/ 0 0 1-iscale.txt >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale
. t x t > --subsample 200 --lta >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
> > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> as > movable/source volume. > --mov: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
> converting source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
> to > bspline ... > MRItoBSpline degree 3 > reading source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
> converting source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
> to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <mailto:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
hello experts
i solve the problem
always thanks your reply
2016-04-30 0:18 GMT+09:00 A-reum Min naniyaah@gmail.com:
hi experts
i have some problem using qdec
when i enter the qdec and then 'Generate Stats Data Tables'
show up these sentences
asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 dep_17 dep_18 dep_19 dep_20 dep_21 dep_22 SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep Parsing the .stats files ERROR: The stats file /usr/local/freesurfer/subjects/HCP_sleep/con_12/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
and show up error box(fig1.jpg)
how can i to do.. plz help me.
my data information is
1 diagnosis discrete 2 1 Control 2 Deprivation 2 age continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 28.167 3.280
Number of subjects: 66 Number of factors: 2 (1 discrete, 1 continuous) Number of classes: 2 Number of regressors: 4
rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 -1 0 0)
2016-03-05 0:36 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning^[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4
, Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&r... patients
exhibit an increase in cortical thickness of about 5-10% in some regions ^[5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5
, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions^[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6
. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the corticalthickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into thefsaverage
space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com> > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm... > Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
> #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> --average 1 --template >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> --satit > --inittp 1 --fixtp --noit --iscale >--iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig
/ 0 0 1-iscale.txt >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale
. t x t > --subsample 200 --lta >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
>/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
> > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> as > movable/source volume. > --mov: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using >/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
> converting source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
> to > bspline ... > MRItoBSpline degree 3 > reading source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
> converting source >'/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
> to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <mailto:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello experts.
I have some question to you.
I used SurfStat statistical tool to analyze the two group(control, patient)
When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg.
What is the differences between lh.pial and lh.pial_avg ?
2016-04-30 0:21 GMT+09:00 A-reum Min naniyaah@gmail.com:
hello experts
i solve the problem
always thanks your reply
2016-04-30 0:18 GMT+09:00 A-reum Min naniyaah@gmail.com:
hi experts
i have some problem using qdec
when i enter the qdec and then 'Generate Stats Data Tables'
show up these sentences
asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 dep_17 dep_18 dep_19 dep_20 dep_21 dep_22 SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep Parsing the .stats files ERROR: The stats file /usr/local/freesurfer/subjects/HCP_sleep/con_12/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
and show up error box(fig1.jpg)
how can i to do.. plz help me.
my data information is
1 diagnosis discrete 2 1 Control 2 Deprivation 2 age continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 28.167 3.280
Number of subjects: 66 Number of factors: 2 (1 discrete, 1 continuous) Number of classes: 2 Number of regressors: 4
rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 -1 0 0)
2016-03-05 0:36 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: While Alzheimer's disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning^[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4>
, Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1> patients
exhibit an increase in cortical thickness of about 5-10% in some regions ^[5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>
, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions^[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>
. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the corticalthickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into thefsaverage
space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com > <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm...
> Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm...
> Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
> #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig
/ 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale
. t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
> > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
> converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
> to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
> converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
> to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <mailto:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hello experts.
I have some question to you.
I used SurfStat statistical tool to analyze the two group(control, patient)
When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg.
What is the differences between lh.pial and lh.pial_avg ?
2016-09-21 20:37 GMT+09:00 A-reum Min naniyaah@gmail.com:
Hello experts.
I have some question to you.
I used SurfStat statistical tool to analyze the two group(control, patient)
When i click the surf in fsaverage folder and then show up lh.pial and lh.pial_avg.
What is the differences between lh.pial and lh.pial_avg ?
2016-04-30 0:21 GMT+09:00 A-reum Min naniyaah@gmail.com:
hello experts
i solve the problem
always thanks your reply
2016-04-30 0:18 GMT+09:00 A-reum Min naniyaah@gmail.com:
hi experts
i have some problem using qdec
when i enter the qdec and then 'Generate Stats Data Tables'
show up these sentences
asegstats2table --common-segs --meas volume --tablefile /usr/local/freesurfer/subjects/HCP_sleep/qdec/stats_tables/aseg.volume.stats.dat --statsfile=aseg.stats --subjects con_1 con_2 con_3 con_4 con_5 con_6 con_7 con_8 con_9 con_10 con_11 con_12 con_13 con_14 con_15 con_16 con_17 con_18 con_19 con_20 con_21 con_22 con_23 con_24 con_25 con_26 con_27 con_28 con_29 con_30 con_31 con_32 con_33 con_34 con_35 con_36 con_37 con_38 con_39 con_40 con_41 con_42 con_43 con_44 dep_1 dep_2 dep_3 dep_4 dep_5 dep_6 dep_7 dep_8 dep_9 dep_10 dep_11 dep_12 dep_13 dep_14 dep_15 dep_16 dep_17 dep_18 dep_19 dep_20 dep_21 dep_22 SUBJECTS_DIR : /usr/local/freesurfer/subjects/HCP_sleep Parsing the .stats files ERROR: The stats file /usr/local/freesurfer/subjects /HCP_sleep/con_12/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files
and show up error box(fig1.jpg)
how can i to do.. plz help me.
my data information is
1 diagnosis discrete 2 1 Control 2 Deprivation 2 age continuous 0 Continuous Factors: Mean: StdDev: ------------------- ----- ------- age 28.167 3.280
Number of subjects: 66 Number of factors: 2 (1 discrete, 1 continuous) Number of classes: 2 Number of regressors: 4
rh--Avg-thickness-age-Cor.mtx and lh-Avg-thickness-age-Cor.mtx contain (1 -1 0 0)
2016-03-05 0:36 GMT+09:00 Douglas N Greve greve@nmr.mgh.harvard.edu:
for asymmetryc, see https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi
On 03/04/2016 09:28 AM, A-reum Min wrote:
hello experts
i have some question to you
Question 1. i want to compare two groups(patients group VS control groups) for cortical thickness asymmetry. so.. am i using a lh.thickness.fsaverage.mgh and rh.thickness.fsaverage.mgh for each group subjects right..?
Question 2.
Left hemisphere whole vertices were extracted using a matlab. ( i read lh.thickness.fsaverage.mgh) i was wondering why vertex# 9(cortical thickness) value is zero? (fig1.png) what is that mean? plz answer me.
2016-02-13 5:19 GMT+09:00 A-reum Min <naniyaah@gmail.com mailto:naniyaah@gmail.com>:
hello experts i have some question to you What is the meaning about cortical thickness alteration (increase or decrease) a few days ago i read these sentences Deviations from these patterns can be used as diagnostic indicators for brain disorders <http://en.citizendium.org/wiki/Brain_disorder>: WhileAlzheimer's
disease <http://en.citizendium.org/wiki/Alzheimer%27s_disease>, even very early on, is characterized by pronounced cortical thinning^[4] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Dickerson2009-4>
, Williams syndrome <http://en.citizendium.org/wiki?title=Williams_syndrome&action=edit&redlink=1> patients
exhibit an increase in cortical thickness of about 5-10% in some regions ^[5] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Thompson2005-5>
, and lissencephalic <http://en.citizendium.org/wiki/Lissencephalic> patients show drastic thickening, up to several centimetres in occipital regions^[6] <http://en.citizendium.org/wiki/Cortical_thickness#cite_note-Guerrini2006-6>
. from wiki i wonder increased or reduced cortex depended on disorder? plz answer me 2016-02-06 0:27 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu
<mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum we use average Euclidean distance from gray to white and visa-versa. There are other (variational) techniques that we have messed around with, but none of our experiments have shown that they are any better, so we have stuck with the simplest thing. cheers Bruce On Fri, 5 Feb 2016, A-reum Min wrote: hello experts i have some question to you What method do you use when measuring the corticalthickness?
(ex. Euclidean distance of a Danielsson Distance Map or 3D Eikonal equation?) plz answer me. 2016-01-17 0:53 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Thank you for u r answer. I have some question to you. i compared two groups(patients VS control) How can i extract the total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(patient) and average of patients ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-17 0:22 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi Areum every brain will have a somewhat different number of vertices depending on size and geometry. If you want them to be comparable you need to map them into thefsaverage
space using e.g. the -qcache switch to recon-all (or mri_surf2surf directly if you prefer). cheers Bruce On Sat, 16 Jan 2016, A-reum Min wrote: Hello expert. I'm Areum. I have some question to you. A weeks ago, i compared two groups (OSA patients VS control) and then the number of vertices were confirmed. Each group has the same number of vertices.(176416) -experiment 1. And yesterday, i compared two groups(partial sleep deprivation:PSD VS control) and then the number of vertices were confirmed. Each group has the same number of vertices(169548) -experiment 2. 1) Why isn't the same number of total vertices? is it related rain size? 2) How can i extract the number of total vertices(ex.#1 vertex : cortical thickness value) to 1 subject(PSD) and average of PSD ? I want to compared asymmetry of brain (lateralization). So, i really necessary above value(cortical thickness value of vertex). plz answer me. Thank you. 2016-01-07 3:52 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum did you talk to the Wash U group? If you have nifti files they can be processed using recon-all (i.e. recon-all -i <full path to nifti file> -s <subject id> -sd <directory to contain all subjects> -all) cheers Bruce On Tue, 29 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you.i have never seen before these NIFTI format(fig.1.png) I want to see these data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-12-25 2:16 GMT+09:00 Bruce Fischl <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>: Hi A-reum you should probably ask the Wash U HCP group. I'll cc Matt Glasser who might be able to answer your question cheers Bruce On Thu, 24 Dec 2015, A-reum Min wrote: hello experts!my name is areum. i have some question to you. a few days ago i was down load HCP(human connectom project) data. but.. how can i use these HCP format. i have never seen before these format(fig.1.png) I want to see HCP data subjects's cortical thickness using qdec. how can i to do? plz answer me 2015-11-10 7:49 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>>: Hello experts! I have some question to you.. I don't need to show up so small blue regions(fig.1 blue region) How can i control these? 2015-11-10 7:41 GMT+09:00 Douglas N Greve <greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>>: Hi, please create a new thread since this is a new topic. Also, I don't understand your question so please elaborate. On 11/09/2015 05:34 AM, A-reum Min wrote: > Hello experts! > > i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > 2015-11-08 20:44 GMT+09:00 A-reum Min <naniyaah@gmail.com <mailto:naniyaah@gmail.com>
> <mailto:naniyaah@gmail.com <mailto:naniyaah@gmail.com>>>: > > Hello bruce! > > I solve the problem for your answer. > > And.. i have some question to you.. > > How can i control the cluster size? > > My cluster threshold is 1. > > then, too many blue regions (as shown fig.1). > > so, i want to control cluster threshold 1--> cluster threshold 5. > > How can i to do? > > > > > > 2015-11-05 22:22 GMT+09:00 Bruce Fischl > <fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu> <mailto:fischl@nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>>>: > > are /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > and /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > images from *different* series or from the *same* series? If > they are in the same series than that explains what is > happening. You should only give recon-all a single file from > any one acquisition - it will figure out the rest of the files > that are part of it. > > cheers > Bruce > > > On Thu, 5 Nov 2015, A-reum Min wrote: > > hello experts. > i have some question to you... > > when i enter the recon-all -i /paht~ > > error showed up.... like below one.. > > how can i to fix it? > > [areum@localhost 0165766_1]# recon-all -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm -i > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > -all -s sub002 > Subject Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > Current Stamp: > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > INFO: SUBJECTS_DIR is > /usr/local/freesurfer/subjects/OSA/0165766_1 > Actual FREESURFER_HOME /usr/local/freesurfer > Linux localhost.localdomain 2.6.32-504.el6.x86_64 #1 SMP > Wed Oct 15 04:27:16 > UTC 2014 x86_64 x86_64 x86_64 GNU/Linux > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm...
> Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016001.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz...
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > > mri_convert > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter > Exp $ > reading from > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm...
> Starting DICOMRead2() > dcmfile = > /usr/local/freesurfer/subjects/OSA/0165766_1/P016002.dcm > dcmdir = /usr/local/freesurfer/subjects/OSA/0165766_1 > Ref Series No = 3 > Found 247 files, checking for dicoms > Found 244 dicom files in series. > First Sorting > Computing Slice Direction > Vs: -0.8 0 0 > Vs: -1 0 0 > Second Sorting > Counting frames > nframes = 1 > nslices = 244 > ndcmfiles = 244 > PE Dir = ROW (dicom read) > TransferSyntaxUID: --1.2.840.10008.1.2.1-- > Loading pixel data > TR=7.70, TE=3.37, TI=400.00, flip angle=12.00 > i_ras = (0, -1, 0) > j_ras = (0, 0, -1) > k_ras = (1, -0, 0) > writing to > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz...
> #-------------------------------------------- > #@# MotionCor Thu Nov 5 02:27:17 PST 2015 > Found 2 runs > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> Checking for (invalid) multi-frame inputs... > Checking for (invalid) multi-frame inputs... > #----------------------------------------------- > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002 > > mri_robust_template --mov > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> --average 1 --template > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> --satit > --inittp 1 --fixtp --noit --iscale > --iscaleout/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig
/ 0 0 1-iscale.txt > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002-iscale
. t x t > --subsample 200 --lta > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.lta
> /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.lta
> > > $Id: mri_robust_template.cpp,v 1.37.2.2 2012/10/10 > 19:59:06 mreuter Exp $ > > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz
> as > movable/source volume. > --mov: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz
> as > movable/source volume. > Total: 2 input volumes > --average: Using method 1 for template computation. > --template: Using > /usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/rawavg.mgz
> as > template output volume. > --satit: Will estimate SAT iteratively! > --inittp: Using TP 1 as target for initialization > --fixtp: Will map everything to init TP! > --noit: Will output only first template (no iterations)! > --iscale: Enableing intensity scaling! > --iscaleout: Will perform intensity scaling and output results > --subsample: Will subsample if size is larger than 200 on > all axes! > --lta: Will output LTA transforms > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'...
> converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/001.mgz'
> to > bspline ... > MRItoBSpline degree 3 > reading source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'...
> converting source > '/usr/local/freesurfer/subjects/OSA/0165766_1/sub002/mri/orig/002.mgz'
> to > bspline ... > MRItoBSpline degree 3 > > MultiRegistration::initializing Xforms (init 1 , maxres 0 > , iterate 5 , > epsit 0.01 ) : > > [init] ========================= TP 2 to TP 1 > ============================== > Register TP 2 ( > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- *------------------------------------------------------------* *Areum Min* Medical Image Processing Lab. Department of Biomedical Engineering, Yonsei Univ. 218 San-hak Hall, 1 Yeonsedae-gil, Heungeop-myeon, Wonju, Gangwon, Korea Office : +82-33-760-2499 Mobile : +82-10-3428-0608 E-Mail : n <mailto:esthekr@nate.com>aniyaah@gmail.com <mailto:aniyaah@gmail.com>
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