New subject: TRACULA

12 Apr 2016

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
<javascript:_e(%7B%7D,'cvml','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
    <javascript:_e(%7B%7D,'cvml','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
        <javascript:_e(%7B%7D,'cvml','ezra_wegbreit@brown.edu');>
        afrancis@mclean.harvard.edu
        <javascript:_e(%7B%7D,'cvml','afrancis@mclean.harvard.edu');>

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

    --
    Jasmin Alves
    Predoctoral Student
    Medical Biology Graduate Program
    University of Southern California
    jalves@usc.edu <javascript:_e(%7B%7D,'cvml','jalves@usc.edu');>

--
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|**
*
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
<javascript:_e(%7B%7D,'cvml','ezra_wegbreit@brown.edu');>
afrancis@mclean.harvard.edu
<javascript:_e(%7B%7D,'cvml','afrancis@mclean.harvard.edu');>

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

Re: [Freesurfer] TRACULA