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 jalves@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 alandarkenergy@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
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*Alan N. Francis PhD* Instructor - Imaging Neuroscience Brain Imaging Center McLean Hospital Harvard Medical School 115 Mill Street, Belmont, MA 02478 alanf@bwh.harvard.edu ezra_wegbreit@brown.edu afrancis@mclean.harvard.edu
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-- Jasmin Alves Predoctoral Student Medical Biology Graduate Program University of Southern California jalves@usc.edu