<p dir="ltr">Hi Matteo,</p>
<p dir="ltr">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...</p>
<p dir="ltr">In any case, the general idea (as documented in <a href="http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks">http://www.brain.org.au/software/mrtrix/faq.html#normalise_tracks</a>) 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...</p>
<p dir="ltr">Cheers,<br>
Donald</p>
<p dir="ltr">--<br>
Dr J-Donald Tournier (PhD)</p>
<p dir="ltr">Senior Lecturer, Biomedical Engineering<br>
Division of Imaging Sciences & Biomedical Engineering<br>
King's College London</p>
<p dir="ltr">A: Department of Perinatal Imaging & Health, 1st Floor South Wing, St Thomas' Hospital, London. SE1 7EH<br>
T: +44 (0)20 7188 7118 ext 53613<br>
W: <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></p>
<p dir="ltr">Dear MRtrix experts,<br>
i would use the command normalise_tracks with the FNIRT output in FSL.<br>
Do i have to use the fields coefficients output in the<br>
normalise_tracks? When i tried this way i got a smaller .tck than the<br>
original one (200M --> 600K) and i don't think it is correct! :)<br>
thank you very much!<br>
Regards</p>
<p dir="ltr">Matteo<br>
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