Hi Doug
Attached is a label file.
The FS version is freesurfer-Darwin-lion-stable-pub-v5.3.0
Here's some background information, that might be helpful.
We had 5 label files (2 for rh and 3 for lh) and 600 subjects.
I batched 600 subjects to run for each label file with the mris_anatomical_stats command.
It successfully ran for ~500 subjects. ~60 subjects didnt run at all across all 5 labels. and then there are ~40 subjects that ran for some labels and didnt run for some and I dont really see a pattern. All 100 subjects that didnt run(60 that didnt run at all and 40 that ran for some labels) all had the segmentation error.
Thank you for you help!
rupa
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Can you verify that the label does actually have label points in it? Just open it in a text editor or cat it to a terminal. If it does have points, send it to me. Also let me know which version of FS you are running.
doug
On 3/17/14 5:35 PM, Rupa Sabbineni wrote:
- muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l
*>* new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh *>* limiting computations to label *>* /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. *>* computing statistics for each annotation in aparc.a2009s.annot. *>* outputting results to outSUB1_lhVOL2... *>* reading volume *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... *>* reading input surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading input pial surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... *>* reading input white surface *>* /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... *>* reading colortable from annotation file... *>* colortable with 76 entries read (originally *>* /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) *>* Segmentation fault: 11 *>>>* On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni <asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer *>* <mailto:asabbineni at mrn.org https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer>> wrote: *>>* Good morning! *>>>* I was trying to run the mris_anatomical_stats command and for some *>* subjects I keep getting Segmentation fault:11 error. *>>* Some of the posts in the archive suggested that I run the *>* recon-all command since it usually means that subjects surfaces *>* are out of sync SO I RERAN RECON_ALL(which created the stats). *>* Then I reran the mris_anatomical_stats command and got the *>* segmentation fault again. *>>>* The command im using is *>>* mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log *>* outSUB1_lhVOL2 SUB1 lh *>>>* A little background on the new.label. We got the label by doing a *>* regression in qdec at FDR 0.05 which created cluster and peak *>* cluster label. *>>>* Can anyone please provide me some insight on how to trouble shoot *>* this problem? *>>* Thank you! *>>* Rupa *>>>>>* -- *>* Rupa *>
On Mon, Mar 17, 2014 at 3:35 PM, Rupa Sabbineni asabbineni@mrn.org wrote:
muen223-105-dhcp:subjects rupasabbineni$ mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh limiting computations to label /Volumes/DISK/Software/freesurfer/subjects/qdec/Results/new.label. computing statistics for each annotation in aparc.a2009s.annot. outputting results to outSUB1_lhVOL2... reading volume /Volumes/DISK/Software/freesurfer/subjects/SUB1/mri/wm.mgz... reading input surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading input pial surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.pial... reading input white surface /Volumes/DISK/Software/freesurfer/subjects/SUB1/surf/lh.white... reading colortable from annotation file... colortable with 76 entries read (originally /autofs/space/birn_044/users/christophe_atlas_rebuild//scripts_2008/Simple_surface_labels2009.txt) Segmentation fault: 11
On Mon, Mar 17, 2014 at 11:54 AM, Rupa Sabbineni asabbineni@mrn.orgwrote:
Good morning!
I was trying to run the mris_anatomical_stats command and for some subjects I keep getting Segmentation fault:11 error.
Some of the posts in the archive suggested that I run the recon-all command since it usually means that subjects surfaces are out of sync SO I RERAN RECON_ALL(which created the stats). Then I reran the mris_anatomical_stats command and got the segmentation fault again.
The command im using is
mris_anatomical_stats -l new.label -a aparc.a2009s.annot -log outSUB1_lhVOL2 SUB1 lh
A little background on the new.label. We got the label by doing a regression in qdec at FDR 0.05 which created cluster and peak cluster label.
Can anyone please provide me some insight on how to trouble shoot this problem?
Thank you!
Rupa
-- Rupa