We certainly cannot guarantee that tkmedit will work as that is a pretty old
program. Try using tkmeditfv in a newer version of FS. It will be ok as long as
the analysis (eg, recon-all, preproc-sess, etc) was done in 5.1
On 11/18/2020 12:00 PM, Tracy Riggins wrote:
External Email - Use Caution
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<mailto: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:
]
--
Tracy Riggins, Ph.D.
Associate Professor
Secretary, Cognitive Development Society
Department of Psychology
4094 Campus Drive
Biology/Psychology Building Room 2147J
University of Maryland
College Park, MD 20742
(301) 405-5905
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