Hi,
We have previously run recon-all -all on 72 subjects using Freesurfer v. 4.01. After routine edits we reprocessed the subjects.
I now want to run the scans again using the updated FS v. 4.05 using the recon-all -all command. We want to have them processed in the latest version in order to do longitudinal analyses.
However, when I run the v. 4.01-processed scans again, using v.4.05 I get the following error in the normalization2 part of the autorecon2 step:
#@# Intensity Normalization2 Fri Oct 10 22:10:06 CEST 2008 /work/1531087.undefined.d/2003A/mri
mri_normalize -aseg aseg.mgz -mask brainmask.mgz norm.mgz brain.mgz
using segmentation for initial intensity normalization reading from norm.mgz... normalizing image... removing outliers in the aseg WM... 68543 control points removed building Voronoi diagram... mriMarkUnmarkedNeighbors: all inputs must be MRI_UCHAR using MR volume brainmask.mgz to mask input volume... using wm (107) threshold 97.0 for removing exterior voxels Linux compute-3-3.local 2.6.9-67.0.15.ELsmp #1 SMP Thu May 8 10:50:20 EDT 2008 x86_64 x86_64 x86_64 GNU/Linux
recon-all exited with ERRORS at Fri Oct 10 22:10:51 CEST 2008
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The same error occurs for all subjects. The error only occurs when I run the subjects on our computing cluster. I have tried to run a couple of scans on a local machine, using the same version. Running locally, I don't get the same error.
We use centOS4 64bit. Any suggestions on how to solve this?
Thanks !
Best regards, Andreas Engvig