[Mrtrix-discussion] Transformations on tracks2prob results

[René Besseling]

Dear MRtrix users,



I’ve experienced some problems in transforming tracks2prob results using
FLSs FLIRT.

What I try to do is to compare the tractography result for two different
scan sessions a and b, e.g. for the corpus callosum (cc). First I define a
seed region in the cc based on the FA map of session a. Using this seed
region I calculate my tracks. Next, I calculate the transform from FAa to
FAb using FSL’s FLIRT. Let’s call this transform FAa2FAb. I use this
transform to convert my session a seed to the session b seed and calculate
my tracks. I convert both tractography results to tract density maps using
tracks2prob. So far so good.

However, in order to check the interscan agreement, I want to transform my
session a track density map to my session b space. I do so by using the
transform FAa2FAb. If I do so, my transformed tract density map is displaced
over several cm with respect to where you would expect it to be looking at
FAb. This is strange since FAb and FAa2FAb nicely agree (proper transform.

I guess this has something to do with the origin of the tract density maps.
Since I want to calculate my tract density maps at a different (higher)
resolution than my FA maps, I don’t use the FA maps as reference but call
tracks2prob with the argument –vox .5. This means the tract density images
are calculated at a 0.5mm grid and tracks2prob automatically determined what
size this grid should be based on the track coordinates. Because in both
sessions different tracks are reconstructed, these grid sizes will differ
between the 2 session. This should not be a problem since the 4x4 FLIRT
transform works on coordinates, not on grids. However, as said, there seems
to be a translational mismatch.



Any ideas on how to solve this? Note that the transformation of my seed from
session a to session b is OK, probably because seeda has the same resolution
and size as FAa.



Best regards,



René Besseling
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