[Mrtrix-discussion] Normalise tracks using output from FNIRT

[Svenja Caspers]

Dear MRtrix experts,
I want to normalise some individual tck-files into MNI-space. I
generated the relevant warp field using FLIRT and FNIRT in FSL. While
this works fine for transforming any individual track density image
(from the command "tracks2prob") into MNI-space, it does not work for
the "normalise_tracks" command.
As suggested in your MRtrix mailing list archives and on the Wiki, I
first generated the nowarp-[].nii files of the template image, using the
"gen_unit_warp" command. Then, I tried to use the "applywarp" command
from FSL to apply the individual warp-field to these three nowarp-[].nii
images. I did that either by applying it to each image alone or by first
concatenating the three images into a single 4D file (using fslmerge)
and then splitting the images back into three warp-[].nii images (using
fslsplit). But neither approach worked out, the normalised tracks look
quite awkward and are completely misplaced.
Do you have any suggestions what I could do to solve this problem?
Any help is very much appreciated!
Thank you very much in advance!
Kind regards,
Svenja


------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------
Forschungszentrum Juelich GmbH
52425 Juelich
Sitz der Gesellschaft: Juelich
Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498
Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher
Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender),
Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt,
Prof. Dr. Sebastian M. Schmidt
------------------------------------------------------------------------------------------------
------------------------------------------------------------------------------------------------