I could be wrong, but the output in your email oscillates between "/Users" and "Users" (Note the preceding forward slash). Im not sure if thats just a copy/paste thing or directly related to your error.
-Zeke On 04/12/2016 08:44 PM, Jasmin Alves wrote: > > > So I have specified where the DTI file is. I am not sure why Tracula > cannot open it. Users/jasminalves/Desktop/data/DTI/40/DTI.nii.gz this is > where the the dti file is. > > > On Tue, Apr 12, 2016 at 11:45 AM, Alan Francis <alandarkene...@gmail.com > <javascript:_e(%7B%7D,'cvml','alandarkene...@gmail.com');>> wrote: > > 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 > <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','ezra_wegbr...@brown.edu');> > afran...@mclean.harvard.edu > <javascript:_e(%7B%7D,'cvml','afran...@mclean.harvard.edu');> > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > > > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jal...@usc.edu <javascript:_e(%7B%7D,'cvml','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 > <javascript:_e(%7B%7D,'cvml','ezra_wegbr...@brown.edu');> > afran...@mclean.harvard.edu > <javascript:_e(%7B%7D,'cvml','afran...@mclean.harvard.edu');> > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > > > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jal...@usc.edu <javascript:_e(%7B%7D,'cvml','jal...@usc.edu');> > > > > -- > Jasmin Alves > Predoctoral Student > Medical Biology Graduate Program > University of Southern California > jal...@usc.edu <mailto:jal...@usc.edu> > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > _______________________________________________ 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. 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