[Mrtrix-discussion] normalise_tracks with FSL

[Donald Tournier]

Hi Matteo,

I'm not sure I completely understand, are you saying that you used the
transformation coefficients produced by fnirt as input to the
normalise_tracks command? I can't see how that can work, normalise_tracks
expects a 4D image with 3 volumes (a vector of new positions in the target
space), so will probably fail if supplied with anything else - unless fnirt
stores its output as an image...? Never used fnirt myself...

In any case, the general idea (as documented in
http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks) is to
get whatever registration package you use to apply the same transform to a
specially crafted image (created using gen_unit_warp), and use the output
of that step as input for normalise_tracks. If this is what you did, it
might help if you could post the commands you used so we can figure out
where things might be going wrong...

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

Dear MRtrix experts,
i would use the command normalise_tracks with the FNIRT output in FSL.
Do i have to use the fields coefficients output in the
normalise_tracks? When i tried this way i got a smaller .tck than the
original one (200M --> 600K) and i don't think it is correct! :)
thank you very much!
Regards

Matteo
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