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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