<div dir="ltr">Hi all,<div><br></div><div>well, in fact, the current implementation of TCK loading in the Fibernav relies on the q-form / s-form of the anatomy that is already loaded. When something like this happens, it is most often caused because the last anatomy that you loaded doesn't have the same affine transform (the s- or q-form) as the one in the anatomy that was used to track your streamlines in Mrtrix.</div><div><br></div><div>As Jan suggested, you could set the affine of your source anatomy to identity before tracking, but that shouldn't be necessary. Instead, just make sure that the last anatomy file you loaded is something that was in the same space as your CSD (or any other model that you used for tracking).</div><div><br></div><div>Best,</div><div><br></div><div><div>--</div><div>Jean-Christophe</div></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">2015-06-18 5:29 GMT-04:00 Jan Schreiber <span dir="ltr"><<a href="mailto:schreiber@cbs.mpg.de" target="_blank">schreiber@cbs.mpg.de</a>></span>:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Hi Jean-Christophe,<br>
<br>
it's probably because the streamlines are in world-coordinates and as far as I know fibernavigator uses voxel coordinates.<br>
<br>
You might get a good result by replacing the transform (s- and q-form if you are using nifti format) with the identity transform before processing the data (be careful if your data is stored in radiologic convention!).<br>
<br>
<br>
Another solution might be to use BrainGL<br>
<a href="https://code.google.com/p/braingl/" rel="noreferrer" target="_blank">https://code.google.com/p/braingl/</a><br>
<br>
Hope that helps,<br>
Jan<div class="HOEnZb"><div class="h5"><br>
<br>
<br>
On 06/18/2015 10:11 AM, Hak Fujiyama wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Jean-Christophe,<br>
<br>
I have been searching for answers to my issue with the visualizations of<br>
tracts created by MRTRIX. I came across your post on the<br>
Mrtrix-discussion and thought that you may be kindly help me.<br>
<br>
I am trying to visualize tracts created by mrtrix with fibernavigator.<br>
<br>
But somehow our tracts doesn’t align with the individual T1 image<br>
(please see attached “m1-m1tckWithT1FiberNav.JPG”), though it does in<br>
Mrview (please see attached “m1-m1tckWithT1mrtrix.JPG”).<br>
<br>
I would appreciate if you could help me on this issue.<br>
<br>
Thank you for your help in advance.<br>
<br>
Best regards,<br>
<br>
Hak<br>
<br>
</blockquote>
<br>
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