[Mrtrix-discussion] DTI fiber measures

[Donald Tournier]

Hi Supreet,

It depends exactly what you're trying to do. There's basically two ways in
MRtrix to extract DTI measures for a given tract. In both cases you'll need
to create maps of the parameters you're interested in: tensor_metric is
probably what you're looking for there.

One way to get the values from the track is to create a mask of the tract
using tracks2prob, then thresholding the resulting image at an appropriate
level. You can then use the resulting binary mask image as the -mask in
mrstats, with any map you might be interested in as the main argument to
that command. That basically gives you the mean value of the parameter of
interest over all voxels visited by the track.

The other way is to use the combination of resample_tracks and
sample_tracks. The first of these 'chops up' the tracks at equivalent
locations along a given straight line (or if needed an arc of a circle),
the second reads the values of a given parameter map at those locations and
stores them in a text file, which you can then load up in Excel, Matlab, R,
or whatever package you want. To use resample_tracks, it helps to use
MRView to get suitable locations for the end points. There's also ways to
use it for group analyses by specifying the end points in some template
space, and providing the warp image that maps that subject to template
space - see Groeschel et al, Neuroimage 2013 for details:
http://www.ncbi.nlm.nih.gov/m/pubmed/24185027/

Hope that provides enough information to get going...
Cheers,

Donald

--
Dr J-Donald Tournier (PhD)

Senior Lecturer, Biomedical Engineering
Division of Imaging Sciences & Biomedical Engineering
King's College London

A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St
Thomas' Hospital, London. SE1 7EH
T: +44 (0)20 7188 7118 ext 53613
W:
http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering

On 23 May 2014 20:11, "Supreet kaur" <ksupreet6 at gmail.com> wrote:

> Dear Mrtrix users,
>
>
> I have been running the CSD and was trying to get the fiber statistic and
> DTI fiber  measures such as FA, MD, eigenvalues, RD and AD values the CSD.
>
> Is there any specific commands that need to be used in order to get these
> DTI measures?
>
>  I'll appreciate your response.
>
> Thanks in advance,
>
>
>
> Sincerely,
>
> Supreet kaur,
> Biomedical research engineer,
> Nationwide Childrens Hospital,
> Columbus, OH
> (614)355-6659.
>
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> Mrtrix-discussion at www.nitrc.org
> http://www.nitrc.org/mailman/listinfo/mrtrix-discussion
>
>
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