CIFTI space output RPI orientation #2118
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@saigerutherford the CIFTI subcortical orientation has been changed to be compatible with HCP analysis in the upcoming 20.1.0 LTS release. The latest release candidate |
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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.
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@saigerutherford now that 20.1.0 has been released, could you try running one participant and see if the orientation is fixed? |
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@saigerutherford could you reopen this issue if you see we really didn't fix it? Also confirming this worked for you would be great, but I'll close this issue for now. |
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The HCP task analysis scripts require the subcortical volumetric data to have RPI orientation, but the fMRIPrep (version 20.0.4) CIFTI output has LPI orientation for the subcortical volumetric data which creates an error when merging the task contrast maps back into CIFTI space (the script splits the CIFTI file into surface & volume, runs task analysis, then merges back together). If anyone would like to run HCP task analysis on this data they need to flip the subcortical data to be RPI orientation in order for the HCP task scripts to work.
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