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 ayendiki@nmr.mgh.harvard.edu 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 <path-to-dmrirc-config-script>', 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. '<subject ID>/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 KuoThe information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.