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,

On Tue, Oct 14, 2014 at 9:53 PM, Douglas Greve <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
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Vy Dinh

MD Candidate, Class of 2017
University of Wisconsin School of Medicine and Public Health