Hmmm, I can't replicate this error. This is 5.3 I assume? doug
On 11/12/2013 06:02 PM, Michael Waskom wrote:
sorry, unclear why the original email wasn't included in the reply. copied here:
I'm running into a strange seg fault when trying to use mri_segstats (it's actually ocurring within mri_glmfit-sim, but I can reproduce it manually)
This is the line that fails (stripping the leading paths for readability):
mri_segstats --seg cache.th20.pos.sig.ocn.mgh --exclude 0 --i concat_output.nii.gz --sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat
With the log:
$Id: mri_segstats.c,v 1.75.2.9 2013/02/16 00:09:33 greve Exp $ cwd cmdline mri_segstats --seg /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh --exclude 0 --i /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz --sum mri_glmfit-sim.junk.84357 --avgwf cache.th20.pos.y.ocn.dat sysname Darwin hostname ben-octocore.stanford.edu http://ben-octocore.stanford.edu/ machine i386 user mwaskom UseRobust 0 Loading /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/osgm/cache.th20.pos.sig.ocn.mgh Loading /Users/mwaskom/Studies/PUnCH/cache/punch-switch_control/fsaverage_group/_l1_contrast_decision_neg/_hemi_lh/glmfit/_glm_results/concat_output.nii.gz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 5 segmentations Computing statistics for each segmentation 1 1 10934 10934.000 2 2 2409 2409.000 3 3 1620 1620.000 4 4 2044 2044.000
Reporting on 4 segmentations Computing spatial average of each frame 0 1 2 3Segmentation fault
Intriguingly, it does not segfault if I remove the --avgwf parameter OR the --exclude 0 parameter. It does segfault if I use --avgwfvol instead of --avgwf
I'm not too sure what's going on, I can otherwise read the segmentation file and --y file and do statistical operations on them, and I can write other files to the directory I'm testing this in.
Here's my system info:
FREESURFER_HOME: /usr/local/freesurfer/5.3.0
Build stamp: freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0
Kernel info: Darwin 10.8.0 i386
Any thoughts?
On Tue, Nov 12, 2013 at 1:36 PM, Douglas N Greve <greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu> wrote:
sorry, what is this in response to? On 11/06/2013 08:13 PM, Michael Waskom wrote: Hi Doug, I can't discern anything off about these images, but I hope it's easy to figure out! They can be downloaded from here ; I figured that was easiest. Michael -- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> Phone Number: 617-724-2358 <tel:617-724-2358> Fax: 617-726-7422 <tel:617-726-7422> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ 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.