Thank you Doug. I was using the same label file for all subjects before. I will create the labels for each individual and run the mris_anatomical_stats ( I tested it on one subject that didnt run before, and it did not give any errors this time) Thanks again! Rupa
**** It looks like this label was created on fsaverage. Is that the case? If so, then you need to run mri_label2label to map it into the space of an individual, then run mris_anatomical_stats doug On 03/18/2014 12:59 PM, Rupa Sabbineni wrote: >* Hi Doug* On Tue, Mar 18, 2014 at 10:59 AM, Rupa Sabbineni <asabbin...@mrn.org> wrote: > 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 > > > *************** > > 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 <asabbin...@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 <asabbin...@mrn.org>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 >> > > > > -- > Rupa > -- Rupa
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