It looks to me like there was an error at an earlier stage, in the -prior
step, so some of the files that the -path step is looking for are not
correct. Look for "img2imgcoord: Command not found." That's a command from
FSL that it can't find. (The 5.2 version of trac-all will not use this any
more, BTW.)
On Mon, 25 Feb 2013, Susan Kuo wrote:
Yes - I'm attaching the trac-all.log. The failure occurred right above this
line:
'trac-paths finished without error at Mon Feb 25 14:08:44 EST 2013'
if you want to search through the text.
The terminal actually showed 2 errors (only the second is recorded in
trac-all.log:
1 - 'Segmentation fault (core dumped)' ---mentioned previously
and
2 - 'ERROR: must specify input volume(s)' -- which I receive after the
program tries to run the below command,
***
/usr/local/freesurfer/bin/dmri_mergepaths
--indir/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa
th --in
--out/j/dti7/Susie/freesurfer/TRACULA_proj/subjects/diffusion_trac/Ca69875.5/dpa
th/merged_avg33_mni_flt.mgz --ctab
/usr/local/freesurfer/FreeSurferColorLUT.txt --thresh .15
ERROR: must specify input volume(s)
***
I'm currently re-running priors and using 32 training subjects plus the
subject's data. Any insight you can offer would be appreciated.
Thank you for your help!
Susie
On Mon, Feb 25, 2013 at 3:47 PM, Anastasia Yendiki
wrote:
Hi Susan - Can you please send your entire trac-all.log? I'll
need to see what else was going on before the error message
occurred.
Thanks,
a.y
On Mon, 25 Feb 2013, Susan Kuo wrote:
Hi FreeSurfer Community, I am trying to run
TRACULA's last step,
'trac-all -path -c ',
and am receiving the
error:
Segmentation fault(core dumped)
Moreover, when I look to standard output (terminal),
I noticed that the
initial 'dmri_paths' command is incomplete. The
terminal shows that the
command includes the '--init' switch and several
arguments (e.g. '/dlabel/diff/rh.atr_PP_avg33_mni_flt_cpts_5.txt'),
the last of which is
terminated mid-pathname. Can anyone suggest a reason
why this would be the
case?
Thank you,
Susie Kuo
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