Hi Diandra,
can you send us one of these datasets so we can see if we can track it down?
thanks Bruce On Wed, 21 Jul 2010, Diandra Lucia wrote:
Hi again,
As we process more cases, we've run into four cases that have had the same problem. Each has segfaulted during mri_segment during autorecon2; here is one example:
#@# Mask BFS Mon Jul 19 23:38:35 EDT 2010 /home/pnlstaff/freesurfer/subjects/case2403/mri
mri_mask -T 5 brain.mgz brainmask.mgz brain.finalsurfs.mgz
threshold mask volume at 5 Writing masked volume to brain.finalsurfs.mgz...done. #-------------------------------------------- #@# WM Segmentation Mon Jul 19 23:38:41 EDT 2010
mri_segment brain.mgz wm.seg.mgz
doing initial intensity segmentation... using local statistics to label ambiguous voxels... computing class statistics for intensity windows... WM (105.0): 105.7 +- 6.1 [80.0 --> 125.0] GM (72.0) : 71.1 +- 8.6 [30.0 --> 96.0] setting bottom of white matter range to 79.6 setting top of gray matter range to 88.2 doing initial intensity segmentation... using local statistics to label ambiguous voxels... using local geometry to label remaining ambiguous voxels...
reclassifying voxels using Gaussian border classifier...
removing voxels with positive offset direction... smoothing T1 volume with sigma = 0.250 removing 1-dimensional structures... 12443 sparsely connected voxels removed... thickening thin strands.... Segmentation fault Linux compute-2-7.local 2.6.9-34.ELsmp #1 SMP Fri Feb 24 16:56:28 EST 2006 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Mon Jul 19 23:40:24 EDT 2010
They all segfaulted at exactly the same place. These were run with freesurfer-Linux-rh9-stable-pub-v4.2.0 (without the new version of the mri_ca_normalize you sent me recently). Please let me know if you need anything else (data, etc) to help troubleshoot this.
Thanks, Diandra