[Mrtrix-discussion] Normalise tracks using output from FNIRT

[Svenja Caspers]

Hi Donald,
thanks, that helped a lot. I had a mix-up with the warps and inverse 
warps. Now, the tracks look perfectly nice.
Best,
Svenja




Am 29.11.13 12:33, schrieb 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 
> <mailto: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 Engineering
> King's College London/
> /
> /
> /*A:* Department of Perinatal Imaging & Health, 1^st  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/

-- 
*Priv.-Doz. Dr. med. Dr. rer. pol. Svenja Caspers *
Institut für Neurowissenschaften und Medizin (INM-1)
Forschungszentrum Jülich GmbH
52425 Jülich (Deutschland)
Tel.: 02461-611742
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