Hi Jasmin - When replying please cc the FS group so that they may weigh in on the situation. Looking at the log, they key problem appears to be this:
niiRead(): error opening file Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz Tracula is not able to open your DTI.nii.gz Please check this file or pathway. best, Alan On Tue, Apr 12, 2016 at 11:17 AM, Jasmin Alves <jal...@usc.edu> wrote: > Hi Alan, > > Thank you for your reply. I changed the pathway but now have stumbled upon > a new error. I tried looking through the feeds and couldn't really find a > relevant solution. > > Jasmins-MacBook-Pro:data jasminalves$ trac-all -prep -c dmrirc.txt > > INFO: SUBJECTS_DIR is /Users/jasminalves/Desktop/data/FREESURFER > > INFO: Diffusion root is /Users/jasminalves/Desktop/data/FREESURFER > > Actual FREESURFER_HOME /Applications/freesurfer > > trac-preproc -c > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/dmrirc.local -log > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.log -cmd > /Users/jasminalves/Desktop/data/FREESURFER/40/scripts/trac-all.cmd > > #------------------------------------- > > /Applications/freesurfer/bin/trac-preproc > > #------------------------------------- > > #@# Image corrections Tue Apr 12 08:04:37 PDT 2016 > > mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz > > mri_convert Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > /Users/jasminalves/Desktop/data/FREESURFER/40/dmri/dwi_orig.nii.gz > > niiRead(): error opening file > Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz > > $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ > > reading from Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz... > > Darwin Jasmins-MacBook-Pro.local 14.5.0 Darwin Kernel Version 14.5.0: Tue > Sep 1 21:23:09 PDT 2015; root:xnu-2782.50.1~1/RELEASE_X86_64 x86_64 > > trac-preproc exited with ERRORS at Tue Apr 12 08:04:37 PDT 2016 > > Your help would be appreciated. > > Thank you, > > Jasmin > > On Tue, Apr 12, 2016 at 7:26 AM, Alan Francis <alandarkene...@gmail.com> > wrote: > >> Hi Jasmin - >> >> In your dmrirc file , the dcmlist refers to the dicom list. You have put >> the BVEC/BVAL files there. That is not correct. You need to place the >> actual pathway to your niftis in this position. >> >> set subjlist = (40 39 36) >> >> # Input diffusion DICOMs (file names relative to dcmroot) >> # If original DICOMs don't exist, these can be in other image format >> # but then bvecfile and bvalfile must be specified >> # >> set dcmroot = Users/jasminalves/Desktop/data/DTI >> set dcmlist = (40/DTI.nii.gz DTI.bvec DTI.bval 39/DTI.nii.gz DTI.bvec >> DTI.bval 36/DTI.nii.gz DTI.bvec DTI.bval) *<- Pathway to NIFTIS HERE* >> >> Hope this helps, >> >> best, >> >> Alan >> >> >> -- >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> >> *Alan N. Francis PhD* >> Instructor - Imaging Neuroscience >> Brain Imaging Center >> McLean Hospital >> Harvard Medical School >> 115 Mill Street, Belmont, MA 02478 >> al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> >> afran...@mclean.harvard.edu >> >> >> |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| >> > > > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jal...@usc.edu > > -- |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| *Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 al...@bwh.harvard.edu <ezra_wegbr...@brown.edu> afran...@mclean.harvard.edu |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|
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