---------- Forwarded message ---------- From: YoungHoon Kwon yhkn11@gmail.com Date: 2016-07-13 21:10 GMT-04:00 Subject: mri_preproc error To: freesurfer@nmr.mgh.harvard.edu
Hello FreeSurfer Developers,
I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after running. I searched for the solution, but I couldn't find it.
Here's information
Error : Segmentation fault (core dumped)
Input : FS.txt (FSGD file) GroupDescriptorFile 1 Title All Class Male Class Female Input 002_S_4213_A Male Input 002_S_4225_A Male Input 002_S_4262_A Female
command: [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage --hemi lh \ --meas thickness \ --out practice_result.mgh nsubjects = 3 tmpdir is ./tmp.mris_preproc.2677 /localscratch3/test Log file is practice_result.mris_preproc.log Wed Jul 13 19:31:44 EDT 2016 setenv SUBJECTS_DIR /localscratch3/test cd /localscratch3/test /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh
Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.2677 Src lh sphere.reg Trg lh sphere.reg
--------------------------------------------------- #@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 -------------- ----------------------- mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped)
I found some advice from online, and it suggested to run recon-all; however it didn't work. I really don't know what is wrong. Can anyone figure out this error?
1) Versioin : FreeSurfer 5.1 2) Platform : Linux 3) uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Hello Freesurfer Developers,
I'm working on group analysis, and I have done GLM analysis(mris_glmfit) on Linux. Next step is to visualize it, so I followed the instruction from the FsTutorial website.
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
Basically, I ran the commend above, and I got the effor "Unrecognized sub-option flag 'annot_outline'" or "unrecognized sub-opton flag 'overlay_threshold'." I think it's because I'm using old FS version which is 5.1, and the tutorial is based on FS 6.1 version. I tried to use tksurfer, but for some reason, it didn't work. I decided to use a freeview anyway.
On 5.1 version, what do I need to do to visualize them? How should I deal with overlay threshold and annot_outline? Please let me know.
Best regards, Younghoon Kwon
2016-07-14 14:01 GMT-04:00 YoungHoon Kwon yhkn11@gmail.com:
---------- Forwarded message ---------- From: YoungHoon Kwon yhkn11@gmail.com Date: 2016-07-13 21:10 GMT-04:00 Subject: mri_preproc error To: freesurfer@nmr.mgh.harvard.edu
Hello FreeSurfer Developers,
I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after running. I searched for the solution, but I couldn't find it.
Here's information
Error : Segmentation fault (core dumped)
Input : FS.txt (FSGD file) GroupDescriptorFile 1 Title All Class Male Class Female Input 002_S_4213_A Male Input 002_S_4225_A Male Input 002_S_4262_A Female
command: [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage --hemi lh \ --meas thickness \ --out practice_result.mgh nsubjects = 3 tmpdir is ./tmp.mris_preproc.2677 /localscratch3/test Log file is practice_result.mris_preproc.log Wed Jul 13 19:31:44 EDT 2016 setenv SUBJECTS_DIR /localscratch3/test cd /localscratch3/test /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh
Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.2677 Src lh sphere.reg Trg lh sphere.reg
#@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 --------------
mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped)
I found some advice from online, and it suggested to run recon-all; however it didn't work. I really don't know what is wrong. Can anyone figure out this error?
- Versioin : FreeSurfer 5.1
- Platform : Linux
- uname -a : Linux in-rady-neuro11.indyrad.iupui.edu 3.16.2-201.fc20.x86_64
#1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Hi Younghoon,
You can adjust those settings from the GUI after you load the surface and overlays. Just click “Configure Overlay” button on the left panel after you load the overlay.
Best, Ruopeng
On Aug 14, 2016, at 9:41 PM, YoungHoon Kwon yhkn11@gmail.com wrote:
Hello Freesurfer Developers,
I'm working on group analysis, and I have done GLM analysis(mris_glmfit) on Linux. Next step is to visualize it, so I followed the instruction from the FsTutorial website.
freeview -f $SUBJECTS_DIR/fsaverage/surf/lh.inflated:annot=aparc.annot:annot_outline=1:overlay=lh.gender_age.glmdir/lh-Avg-thickness-age-Cor/sig.mgh:overlay_threshold=4,5 -viewport 3d
Basically, I ran the commend above, and I got the effor "Unrecognized sub-option flag 'annot_outline'" or "unrecognized sub-opton flag 'overlay_threshold'." I think it's because I'm using old FS version which is 5.1, and the tutorial is based on FS 6.1 version. I tried to use tksurfer, but for some reason, it didn't work. I decided to use a freeview anyway.
On 5.1 version, what do I need to do to visualize them? How should I deal with overlay threshold and annot_outline? Please let me know.
Best regards, Younghoon Kwon
2016-07-14 14:01 GMT-04:00 YoungHoon Kwon <yhkn11@gmail.com mailto:yhkn11@gmail.com>:
---------- Forwarded message ---------- From: YoungHoon Kwon <yhkn11@gmail.com mailto:yhkn11@gmail.com> Date: 2016-07-13 21:10 GMT-04:00 Subject: mri_preproc error To: freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu
Hello FreeSurfer Developers,
I tried to assemble the data by using mri_preproc, then it shows segmentation fault (core dumped) after running. I searched for the solution, but I couldn't find it.
Here's information
Error : Segmentation fault (core dumped)
Input : FS.txt (FSGD file) GroupDescriptorFile 1 Title All Class Male Class Female Input 002_S_4213_A Male Input 002_S_4225_A Male Input 002_S_4262_A Female
command: [knho@in-rady-neuro11 test]$ mris_preproc --fsgd FS.txt \ --target fsaverage --hemi lh \ --meas thickness \ --out practice_result.mgh nsubjects = 3 tmpdir is ./tmp.mris_preproc.2677 /localscratch3/test Log file is practice_result.mris_preproc.log Wed Jul 13 19:31:44 EDT 2016 setenv SUBJECTS_DIR /localscratch3/test cd /localscratch3/test /net/age3/DATA_from_AGE0/FREESURFER/freesurfer51/bin/mris_preproc --fsgd FS.txt --target fsaverage --hemi lh --meas thickness --out practice_result.mgh
Linux in-rady-neuro11.indyrad.iupui.edu http://in-rady-neuro11.indyrad.iupui.edu/ 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux $Id: mris_preproc,v 1.59.2.1 2011/05/17 03:42:01 greve Exp $ freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 tmpdir is ./tmp.mris_preproc.2677 Src lh sphere.reg Trg lh sphere.reg
#@# 1/3 002_S_4213_A Wed Jul 13 19:31:44 EDT 2016 --------------
mri_surf2surf --srcsubject 002_S_4213_A --srchemi lh --srcsurfreg sphere.reg --trgsubject fsaverage --trghemi lh --trgsurfreg sphere.reg --tval ./tmp.mris_preproc.2677/002_S_4213_A.1.mgh --sval /localscratch3/test/002_S_4213_A/surf/lh.thickness --sfmt curv --noreshape --no-cortex Segmentation fault (core dumped)
I found some advice from online, and it suggested to run recon-all; however it didn't work. I really don't know what is wrong. Can anyone figure out this error?
- Versioin : FreeSurfer 5.1
- Platform : Linux
- uname -a : Linux in-rady-neuro11.indyrad.iupui.edu http://in-rady-neuro11.indyrad.iupui.edu/ 3.16.2-201.fc20.x86_64 #1 SMP Mon Sep 15 19:57:50 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Ruopeng Wang -
YoungHoon Kwon