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 
> <mailto:MailScanner has detected a possible fraud attempt from "mail.nmr.mgh.harvard.edu" claiming to be asabbineni at 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
>

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.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