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Dear Freesurfer Gurus We just upgraded our server to RHEL 7. However, we want to do some white/pial edits on some brains using Freesurfer 5.1.0. We know this is an old version, but we are combining some new data with a lot of old data that had been processed before in 5.1.0 and ... we want to use the old version.
However, when using tkmedit the error below was received.
Can you help? Thanks in advance, Tracy
=================================== ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting...
*Contents of the the file .xdebug_tkmedit here:*
tkmedit started: Wed Nov 18 10:50:06 2020
/cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin SLP003_practice_KK brainmask.mgz -aux wm.mgz -surfs
$Id: tkmedit.c,v 1.343 2011/03/01 01:41:22 nicks Exp $ $Name: stable5 $ Set user home dir to /export/data/seahorse_ncdl/SLP/data/white_pial_practice Set subject home dir to /export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK
Segfault Importing volume with MRIread xDebug stack (length: 5) 04: Volm_ImportData( this=0x27f57890, isSource=/export/data/seahorse_ncdl/SLP/data/white_pial_practice//SLP003_practice_KK/mri/brainmask.mgz ) 04: Importing volume with MRIread 03: LoadVolume( iType=0, isName=brainmask.mgz, ibConform = 0 ) 03: Reading data into volume 02: ParseCmdLineArgs( argc=6, argv=/cell_root/software/freesurfer/5.1.0/sys/tktools/tkmedit.bin ) 02: Loading volume brainmask.mgz 01: main() 01: Parsing command line arguments 00: 00:
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