FIX: Feed *NiTransforms* with LTAs of type RAS2RAS #2444
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The patch does seem to fix the issue locally (using docker, nipreps/fmriprep:20.1.3 and patching in the development sources). |
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Will look in the afternoon EDT. |
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As reported by @eburkevt back in October 18, 2020, resampled BOLD time-series in standard spaces do not look good anymore. This PR uses FreeSurfer to cater RAS2RAS transforms to *NiTransforms*. This may resolved the problem for *fMRIPrep* regardless of the resolution of nipy/nitransforms#125 Addresses: #2307. wq
Co-authored-by: Chris Markiewicz <markiewicz@stanford.edu>
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Worked locally on the reported subject, and CircleCI artifacts look good (screened the report for ds054 and ds210, and screened the boldrefs of each on MNI space). Rushing in the merge. |
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The structarray was used directly and the extra axis actually changed the order of operations when the direction cosines were scaled by the voxel sizes. A new test case has been added for which this error was apparent. This bug caused nipreps/fmriprep#2307, nipreps/fmriprep#2393, and nipreps/fmriprep#2410. nipreps/fmriprep#2444 just works around the problem by using ``lta_convert`` instead of *NiTransforms*. The ``lta_convert`` tool can be now dropped. Resolves: #125
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Porting over fix originally implemented in nipreps/fmriprep#2444
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The new LTA file and the matrix hard-coded on the test come from an issue discovered in *fMRIPrep* (see nipreps/fmriprep#2444). This test currently breaks master.
This was referenced Aug 18, 2021
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As reported by @eburkevt back on October 18, 2020, resampled BOLD time-series in standard spaces do not look good anymore.
This PR uses FreeSurfer to cater RAS2RAS transforms to NiTransforms.
This may resolve the problem for fMRIPrep regardless of the resolution of nipy/nitransforms#125
Addresses: #2307.