Hi Thomas - No bother at all! If you search for the word "error" in your trac-all.log, you'll see that it couldn't find the MNI template, which means that some of the pre-processing steps did not complete. You can either remove the "mnitemp" line from your configuration file (so that it uses the default $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) or edit that line to include the correct path to the MNI template. You'll then need to rerun the pre-processing, or at least the steps including the inter-subject registration and beyond (run trac-all without arguments to see the sequence of steps included in the pre-processing).
Hope this helps, a.y On Wed, 10 Dec 2014, Thomas DeRamus wrote: > Freesurfer Experts, > > Sorry to bother you again, but I'm having an issue with the 3rd step of > Tracula. I was able to run -prep just fine, and I ran bedpostx locally > (there was an error in the step 2 command apparently, used command "bedpostx > /<path>/<subj>/dmri/"), but every time I run the third step with the -path > command I get the error "Segmentation fault (core dumped) foreach: No > match." > > The foreach error has me thinking there is something wrong with my dmrirc > file or my folder structure. > > I'd appreciate any feedback you are willing to give on this error. > > I've attached the trac-all.log for one subject, but it gives the same error > even when different subjects are used or this one is removed. > > -- > Thomas DeRamusUAB Department of Psychology, Behavioral Neuroscience > Graduate Research Trainee > Civitan International Research Center > 1719 6th Ave S, Suite 235J, Birmingham, AL 35233 > Phone: 205-934-0971 Email: tpdera...@gmail.com, faus...@uab.edu > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The 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.
