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 > 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 <*MailScanner has > detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to > be* asabbineni at mrn.org > <https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> > />/ <mailto:*MailScanner has detected a possible fraud attempt from > "mail.nmr.mgh.harvard.edu" claiming to be* 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 > <mailto: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 <mailto: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 > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ _______________________________________________ Freesurfer mailing list 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.
