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oesteban opened this issue Nov 4, 2017 · 3 comments
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Use lta_convert for simplicity #2121

oesteban opened this issue Nov 4, 2017 · 3 comments
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20.3.0

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@oesteban
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oesteban commented Nov 4, 2017 •
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Comes from #745 (comment)

EDIT:
This issue is a reminder that this code:

https://github.com/oesteban/fmriprep/blob/eb3c838f1bed031c9f02d54b3db3bdcae2dad8dd/fmriprep/workflows/bold/registration.py#L455-L463

might be hacky and hard to maintain. A solution using FS' lta_convert or nitransforms would be more sustainable
@oesteban oesteban transferred this issue from nipreps/fmriprep Jan 8, 2019
@effigies
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effigies commented Jan 8, 2019

I thought that was referring to the BOLD-T1w transforms.

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oesteban commented Jan 8, 2019

True, I'll roll the transfer back :( sorry about that.

@oesteban oesteban transferred this issue from nipreps/smriprep May 8, 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 this to the 20.3.x milestone May 28, 2020
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oesteban commented Jun 5, 2020

3903bee

@oesteban oesteban closed this as completed Jun 5, 2020
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