[Mrtrix-discussion] Obtaining tensor-based measures for specific fibre tract (streamline) bundles

[Donald Tournier]

Hi Simon,

You can also sample values at the vertices of each track using the
sample_tracks command. This produces a big text file with rows of values,
one row per track.

This is actually best used in conjunction with the resample_tracks command,
which is designed to regrid the tracks such that the vertices fall at
equivalent levels along it. It's not the best documented command around, so
might take some getting used to, but essentially you can specify a straight
line by its two end points, and the number of sample points to take along
it. Each track will be resampled so its vertices fall on the plane
perpendicular to the line at the specified sample levels. You can also
specify a 'way point' (I think it's called a midpoint in the doc) to have
the resampling done along the corresponding arc of a circle through the
three points, which is useful for curved tracks. Finally, there is a nifty
feature that allows you to specify the endpoints and midpoint on a
template, along with the warp to the subject's native space, which then
allows you to resample at equivalent points in template space without
leaving native space. I won't explain it here, but we used it in a paper
that just got accepted in Neuroimage, I expect it'll be available online
fairly soon (Samuel Groeschel is first author).

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

Hi Simon,
You can use tracks2prob (with the FA map as the template) followed by a
threshold to create mask of your bundle of interest. You can then use
mrstats with the --mask option to compute the mean FA within this mask.
Cheers,
Dave



On 29 October 2013 12:47, Simon Baker <simontebaker at gmail.com> wrote:

> Hi all,
>
> Is there a command that allows us to easily obtain tensor-based measures
> (e.g., mean FA) for specific fibre tract (streamline) bundles? Failing
> that, is there a way to save a mask image of the streamlines so that we can
> use this image to mask the FA map and calculate mean FA? What's the best
> way to obtain these measures?
>
> Thank you,
>
> Simon
>
> --
>
> Simon Baker
> PhD Candidate
> Faculty of Medicine, Nursing and Health Sciences
> Monash University
>
> _______________________________________________
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> Mrtrix-discussion at www.nitrc.org
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>
>


-- 
*David Raffelt (PhD)*
Post Doctoral Fellow

The Florey Institute of Neuroscience and Mental Health
Melbourne Brain Centre - Austin Campus
245 Burgundy Street
Heidelberg Vic 3084
Ph: +61 3 9035 7024
www.florey.edu.au

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