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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