<div dir="ltr">Hi Svenja,<div><br></div><div>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...</div>
<div><br></div><div>Cheers,</div><div>Donald.</div><div><br></div></div><div class="gmail_extra"><br><br><div class="gmail_quote">On 29 November 2013 10:52, Svenja Caspers <span dir="ltr"><<a href="mailto:s.caspers@fz-juelich.de" target="_blank">s.caspers@fz-juelich.de</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear MRtrix experts,<br>
I want to normalise some individual tck-files into MNI-space. I<br>
generated the relevant warp field using FLIRT and FNIRT in FSL. While<br>
this works fine for transforming any individual track density image<br>
(from the command "tracks2prob") into MNI-space, it does not work for<br>
the "normalise_tracks" command.<br>
As suggested in your MRtrix mailing list archives and on the Wiki, I<br>
first generated the nowarp-[].nii files of the template image, using the<br>
"gen_unit_warp" command. Then, I tried to use the "applywarp" command<br>
from FSL to apply the individual warp-field to these three nowarp-[].nii<br>
images. I did that either by applying it to each image alone or by first<br>
concatenating the three images into a single 4D file (using fslmerge)<br>
and then splitting the images back into three warp-[].nii images (using<br>
fslsplit). But neither approach worked out, the normalised tracks look<br>
quite awkward and are completely misplaced.<br>
Do you have any suggestions what I could do to solve this problem?<br>
Any help is very much appreciated!<br>
Thank you very much in advance!<br>
Kind regards,<br>
Svenja<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><div><br></div>-- <br><div dir="ltr"><b><font color="#990000">Dr J-Donald Tournier (PhD)</font></b><br><div><font color="#990000"><br></font></div><i><font color="#990000">Senior Lecturer, </font></i><i><font color="#990000">Biomedical Engineering</font></i><div>
<i><font color="#990000">Division of Imaging Sciences & Biomedical Engineering<br>King's College London</font></i><div><i><font color="#990000"><br></font></i></div><div><i><font color="#990000"><b style="font-family:Calibri,sans-serif;font-size:15px"><span style="font-size:10pt">A:</span></b><span style="font-family:Calibri,sans-serif;font-size:10pt"> Department of Perinatal Imaging & Health, 1<sup>st</sup> Floor South Wing, St Thomas' Hospital, London. SE1 7EH</span><br>
</font></i></div><div><i><font color="#990000"><b>T:</b> +44 (0)20 7188 7118 ext 53613</font></i></div></div><div><i><font color="#990000"><b>W:</b> <a href="http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering" target="_blank">http://www.kcl.ac.uk/medicine/research/divisions/imaging/departments/biomedengineering</a></font></i><br>
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