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LTA concatenation with NiTransforms producing wrong transforms #2145

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oesteban opened this issue May 27, 2020 · 0 comments · Fixed by #2146
Closed

LTA concatenation with NiTransforms producing wrong transforms #2145

oesteban opened this issue May 27, 2020 · 0 comments · Fixed by #2146
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bug CIFTI / Grayordinates critical effort: low Estimated low effort task freesurfer impact: high Estimated high impact task
Milestone
20.1.0

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@oesteban
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A problem using ConcatenateXFMs from the new niworkflows.interfaces.nitransforms module resulted in surface-sampled results looking like:

Screen Shot 2020-05-26 at 4 10 41 PM

because of the sampler receives the wrong transformation.

The problem is easily noticeable on the carpetplot:
image (1)

Thanks @mgxd for catching this and making all the necessary diagnosis.
@oesteban oesteban added the bug label May 27, 2020
@oesteban oesteban added this to the 20.1.0 milestone May 27, 2020
oesteban added a commit to oesteban/fmriprep that referenced this issue May 27, 2020
@oesteban
FIX: Generate proper LTA transform prior BOLD sampling on surfaces
f63af68 
This is a temporary patch before we go all the way in with NiTransforms
in the sampling of BOLD on surfaces.

The anatomical _fast-track_ required to expose the fsnative-to-T1w
transform in the derivatives folder (which we were already doing in ITK
format).

When fMRIPrep ran without the fast-track, then the LTA transform would
be directly passed in without conversions. The fast-track PR forced the
implementation to use the ITK version.

This, in conjunction with the little trick to stick the BOLD shape and
zooms into the LTA (i.e., using ``lta_concatenate`` with an identity
transform with those features, shape and zooms, as moving) resulted in
an overly complex workflow that I partially implemented with
NiTransforms.

This PR gets rid of the concatenation with identity trick, using
NiTransforms to generate a transform equivalent to the concatenated LTA
we used to generate before the fast-track was introduced.

Resolves: nipreps#2145
Assign: @mgxd
Milestone: 20.1.0
Related: nipreps#2118, nipreps#2041, nipreps#2121.
@oesteban oesteban mentioned this issue May 27, 2020
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@oesteban oesteban added CIFTI / Grayordinates critical effort: low Estimated low effort task freesurfer impact: high Estimated high impact task labels May 27, 2020
@mgxd mgxd mentioned this issue May 28, 2020
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FIX: Generate proper LTA transform prior BOLD sampling on surfaces oesteban/fmriprep
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