Excellent! Thanks Anastasia for the info. Melissa Pangelinan, Ph.D. Postdoctoral Research Fellow Rotman Research Institute 3560 Bathurst Street Brain Health Complex Room 904 Toronto, Ontario M6A 2E1 phone: 416.785.2500 x3352 web: http://melissapangelinan.weebly.com/
> On Jun 16, 2015, at 2:32 PM, Anastasia Yendiki <ayend...@nmr.mgh.harvard.edu> > wrote: > > > Hi Melissa - The option to have a different gradient table for each subject > was added after the 5.3 release, in a tracula update: > > http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula#Updates > > If you don't have that update, it's not going to recognize bveclist. > > Best, > a.y > >> On Thu, 11 Jun 2015, Melissa Pangelinan wrote: >> >> Hi, >> I am trying to run trac-all using >> freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 >> If I set up the configuration file with just one subject as a test, trac-all >> runs without errors. However, when I update the configuration >> file for more than one subject, I get the following error: >> mv -f /scratch/mpangeli/DT_Output/MRI_10315/dmri/dwi_orig_flip.mghdti.bvecs >> /scratch/mpangeli/DT_Output/MRI_10315/dmri/bvecs >> mv: cannot stat >> `/scratch/mpangeli/DT_Output/MRI_10315/dmri/dwi_orig_flip.mghdti.bvecs': No >> such file or directory >> Linux gpc-f103n084-ib0 2.6.32-504.3.3.el6.x86_64 #1 SMP Wed Dec 17 01:55:02 >> UTC 2014 x86_64 x86_64 x86_64 GNU/Linux >> trac-preproc exited with ERRORS at Wed Jun 10 23:37:25 EDT 2015 >> The only differences between the two configuration files are: >> 1) Listing all subjects in the "set dcmlist" >> 2) Using "set bveclist" instead of "set bvecfile" >> For example: >> set bvecfile = /scratch/mpangeli/DTI/MRI_10315/MRI_10315.bvecs >> vs. >> set bveclist = (/scratch/mpangeli/DTI/MRI_10315/MRI_10315.bvecs \ >> /scratch/mpangeli/DTI/MRI_10316/MRI_10316.bvecs \ >> /scratch/mpangeli/DTI/MRI_10317/MRI_10317.bvecs \ >> /scratch/mpangeli/DTI/MRI_10318/MRI_10318.bvecs) >> Clearly #2 is the issue (it can't find the bvec files) but I don't know how >> to modify the configuration file to correctly call the list of >> paths to each subject's bvec file. >> Any help on this error is much appreciated. >> -Melissa > _______________________________________________ > 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
