[Mrtrix-discussion] Normalise tracks using output from FNIRT

[Donald Tournier]

Hi Svenja,

You could try to figure out what is going on by running the exact same
applywarp command on an image in template space, to verify that it does
results in the correct alignment of the template in subject space. If this
works OK, and the nowarp images were generated based on the template image,
then I'm not too sure what is going on...

Cheers,
Donald.



On 29 November 2013 10:52, Svenja Caspers <s.caspers at fz-juelich.de> wrote:

> 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
>
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-- 
*Dr J-Donald Tournier (PhD)*

*Senior Lecturer, **Biomedical Engineering*

*Division of Imaging Sciences & Biomedical EngineeringKing's College London*


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Thomas' Hospital, London. SE1 7EH*
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