[Mrtrix-discussion] Transformations on tracks2prob results

[Donald Tournier]

Hi René,

In my (admittedly limited) experience with FLIRT, what *I think* I've
figured out is that the transform matrix maps from image space in A to image
space in B, both expressed in mm relative to their own image axes, not
relative to real (scanner) coordinates. I don't expect it to handle a shift
in the origin of either datasets, or for that matter any differences in
their respective transforms. That said, I'm not 100% sure I fully understand
all this, and I could easily be way off the mark... Maybe others can help
out who have more experience with FSL?

Cheers,

Donald.



2010/10/27 René Besseling <r.m.h.besseling at gmail.com>

> 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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>


-- 
Jacques-Donald Tournier (PhD)
Brain Research Institute, Melbourne, Australia
Tel: +61 (0)3 9496 4078
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