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Hi Donald,<br>
thanks, that helped a lot. I had a mix-up with the warps and inverse
warps. Now, the tracks look perfectly nice.<br>
Best,<br>
Svenja<br>
<br>
<br>
<br>
<br>
<div class="moz-cite-prefix">Am 29.11.13 12:33, schrieb Donald
Tournier:<br>
</div>
<blockquote
cite="mid:CAHgym8+ZinGnNmtt1p1HpQmeBnES=WheOqohjfwSkzAhB8pPew@mail.gmail.com"
type="cite">
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<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 moz-do-not-send="true"
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
moz-do-not-send="true"
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>
</div>
</div>
</div>
</blockquote>
<br>
<div class="moz-signature">-- <br>
<b> Priv.-Doz. Dr. med. Dr. rer. pol. Svenja Caspers </b><br>
Institut für Neurowissenschaften und Medizin (INM-1) <br>
Forschungszentrum Jülich GmbH <br>
52425 Jülich (Deutschland) <br>
Tel.: 02461-611742</div>
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