Can you send your command line with all variables substituted for actual arguments? On 10/15/14 12:26 AM, Vy Dinh wrote:
Hi Dr. Greve,
I'm encountering a "segmentation fault" for some subjects when I run the following command:
mris_anatomical_stats -l $label -t $hemi.volume -b -f $sublabel $sub $hemi
*This is the program output for a subject that had the segmentation fault. Strangly, this occurs with the volume labels only (which are fairly large). *
label: lh.volume.15.age.inferiortemporal.label
sublabel: /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/stats/lh.volume.15.age.inferiortemporal.stats
hemisphere: lh
limiting computations to label lh.volume.15.age.inferiortemporal.label.
using thickness file lh.volume.
reading volume /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/mri/wm.mgz...
reading input surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.white...
reading input pial surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.pial...
reading input white surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029/surf/lh.white...
batch_mris_anatomical_stats.sh: line 75: 31130 *Segmentation fault * (core dumped) mris_anatomical_stats -l $label -t $j.volume -b -f $sublabel $m $j
*This is the program output for a subject that worked. If I wanted to extract other values (e.g. pial surface area, surface area, curvature, sulci), do I need to specify the measurement's corresponding "thickness" file in the mri_anatomical_stats command?*
label: rh.volume.15.age.superiorfrontal.label
sublabel: /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/stats/rh.volume.15.age.superiorfrontal.stats
hemisphere: rh
limiting computations to label rh.volume.15.age.superiorfrontal.label.
using *thickness file rh.volume*.
reading volume /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/mri/wm.mgz...
reading input surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.white...
reading input pial surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.pial...
reading input white surface /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_028/surf/rh.white...
table columns are:
number of vertices
total surface area (mm^2)
total gray matter volume (mm^3)
average cortical thickness +- standard deviation (mm)
integrated rectified mean curvature
integrated rectified Gaussian curvature
folding index
intrinsic curvature index
structure name
7244 4701 14611 1.912 1.468 0.166 0.166 577 36.7 rh.volume.15.age.superiorfrontal.label
subject dir: /Volumes/Vol6/YouthPTSD/data/freesurfer/subjects/_029
Thank you,
Vy
On Tue, Oct 14, 2014 at 9:53 PM, Douglas Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
Use -t hemi.volume (and change the name of the output file:-) doug On 10/14/14 2:30 PM, Vy Dinh wrote:Dear experts, Can one use mri_anatomical_stats to extract volume information? I have a set of labels that has been mapped to each subject's native space (using mri_label2label; the original labels were extracted from group comparisons using mri_glmfit). I have successfully extracted the thickness measures using mri_anatomical_stats and am curious if this can be done with the labels from my volume group comparisons as well. This is the command I used for the extracting the thickness measures: mris_anatomical_stats -l $label -t $hemi.thickness -b -f $sublabel $sub $hemi Thanks in advance, -- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ 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.-- Vy Dinh MD Candidate, Class of 2017 University of Wisconsin School of Medicine and Public Health
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