[Mrtrix-discussion] normalise_tracks with FSL

[Matteo Diano]

Hi Donald,
thank you very much! I followed the instruction using Flirt instead of
Fnirt and it seems working. I also found a previous post
http://www.nitrc.org/pipermail/mrtrix-discussion/2011-January/000165.html
that explain how to use the non linear estimation in SPM.
Cheers

Matteo

2014-03-28 15:25 GMT+01:00 Donald Tournier <jdtournier at gmail.com>:
> 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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