Jasmin -

Check the DTI.nii.gz file using MRICRON and see if the images across the gradients are OK. If the file is corrupt, then Tracula cannot read this.

best,

A

On Tue, Apr 12, 2016 at 8:44 PM, Jasmin Alves <jalves@usc.edu> 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 <alandarkenergy@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 <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


--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|



--
Jasmin Alves
Predoctoral Student 
Medical Biology Graduate Program 
University of Southern California



--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|



--
Jasmin Alves
Predoctoral Student 
Medical Biology Graduate Program 
University of Southern California


--
Jasmin Alves
Predoctoral Student 
Medical Biology Graduate Program 
University of Southern California




--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

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
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|