As an add-on to this, note that using a single table for all subjects is probably only appropriate if the DWI was acquired with a fixed orientation relative to the scanner gradient axes (e.g., strictly axial) for all subjects.  If the orientation was customized individually for each subject (e.g., to align the imaging plane with the AC/PC), then it is unlikely that using a single table for all subjects is appropriate.

cheers,
-MH

-- 
Michael Harms, Ph.D.
-----------------------------------------------------------
Conte Center for the Neuroscience of Mental Disorders
Washington University School of Medicine
Department of Psychiatry, Box 8134
660 South Euclid Ave. Tel: 314-747-6173
St. Louis, MO  63110 Email: mharms@wustl.edu

From: <freesurfer-bounces@nmr.mgh.harvard.edu> on behalf of Alan Francis <alandarkenergy@gmail.com>
Reply-To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Date: Friday, February 5, 2016 at 3:57 PM
To: Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu>
Cc: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: Re: [Freesurfer] DTI - Tracula question

Hi Anastasia:

Thank you so much. Yes that is very helpful.

best,

Alan

On Fri, Feb 5, 2016 at 3:03 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

Hi Alan - Yes, you can give a single file for all data sets if they're all acquired with the same gradient table and slice prescription. As a test, you can extract the gradient tables from a couple of your data set's dicom headers and see how different they are. If there are only very small differences, using a single table for all will not make a difference.

Hope this helps,

a.y


On Fri, 5 Feb 2016, Alan Francis wrote:

Thanks Anastasia - that was very helpful. I have another question :  I am working on a DTI dataset of around 70 subjects. This
dataset has ostensibly only 1 set of BVECS/BVALS. Can this set be 'generically' used for all the images, given that they have been
acquired on the same scanner?

 

thanks,

 

Alan


On Wed, Feb 3, 2016 at 4:17 PM, Anastasia Yendiki <ayendiki@nmr.mgh.harvard.edu> wrote:

      Hi Alan - A nifti file with the gradient tables and b-values embedded? All freesurfer programs can handle nifti
      volumes, compressed (.nii.gz) or not (.nii). You can pass those volumes to TRACULA, and pass the gradient table and
      b-value table as separate files.

      Run "mri_convert --help" to see all image file formats that we can handle.

      Hope this helps,
      a.y

      On Wed, 3 Feb 2016, Alan Francis wrote:

            Hi Anastasia:

            I am working on a set of DTI data that were obtained at the Martinos center. The data is in a single
            nii.gz file. The BVECS and
            BVALS files are also embedded in this. Could you please advice me how do I code this in the DMRIRC file?

            Should I convert the nii.gz file into Analyze to get at the BVECS/ BVALS?

            thank you so much,

            best regards,

            Alan

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

            Alan N. Francis PhD
            NIDA T32  Fellow in Computational Neuroscience
            Brain Imaging Center
            McLean Hospital
            Harvard Medical School
            115 Mill Street, Belmont, MA 02478
            alanf@bwh.harvard.edu
            afrancis@mclean.harvard.edu
                                                                                                                      
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Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
afrancis@mclean.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|




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

Alan N. Francis PhD
NIDA T32  Fellow in Computational Neuroscience
Brain Imaging Center
McLean Hospital
Harvard Medical School
115 Mill Street, Belmont, MA 02478
alanf@bwh.harvard.edu
                                                                                                          
|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|

 

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