[Mrtrix-discussion] Transformations on tracks2prob results

[René Besseling]

Dear all,

I think Donald is right with the relative coordinates; the "mat" structure
related to a 128x128x60 NIFTI with 2mm voxels is [-2 0 0 129; 0 2 0 -129; 0
0 2 -61; 0 0 0 1] and considering the last column this must be a relative
transform from grid to coordinates a not an absolute one.

Anyone any idea whether the absolute coordinates (with respect to the magnet
isocentre or so) are stored in NIFTIs?

Best regards,

René


2010/10/27 Donald Tournier <d.tournier at brain.org.au>

> 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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>> Mrtrix-discussion at www.nitrc.org
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>>
>>
>
>
> --
> Jacques-Donald Tournier (PhD)
> Brain Research Institute, Melbourne, Australia
> Tel: +61 (0)3 9496 4078
>
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