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Enable MSMSulc for improved surface alignment #2694

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effigies opened this issue Jan 20, 2022 · 0 comments · Fixed by #3085
Closed

Enable MSMSulc for improved surface alignment #2694

effigies opened this issue Jan 20, 2022 · 0 comments · Fixed by #3085
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CIFTI / Grayordinates effort: medium Estimated medium effort task feature impact: medium Estimated medium impact task
Milestone
23.x

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@effigies
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What would you like to see added in fMRIPrep?

This thread is for discussion of implementation of MSMSulc for improved surface alignment.

Some initial considerations:

  • Installation: MSM is packaged in FSL 6, so adding to Docker is a matter of whitelisting the necessary files.
  • Default behavior: @edickie said in Support HCP-compatible CIFTI outputs #1025 that it adds significant runtime; should this be on or off by default?

Reference: https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/MSM/UserGuide

Do you have any interest in helping implement the feature?

Yes

Additional information / screenshots

No response
@effigies effigies added feature impact: medium Estimated medium impact task effort: medium Estimated medium effort task CIFTI / Grayordinates labels Jan 20, 2022
@effigies effigies added this to the 22.x milestone Jan 21, 2022
@edickie edickie mentioned this issue Jul 20, 2023
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@effigies effigies modified the milestones: 22.x, 23.x Aug 3, 2023
This was referenced Sep 6, 2023
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effigies added a commit that referenced this issue Sep 7, 2023
@effigies
ENH: Add MSMSulc (#3085)
2065965 
Closes #2694 

This PR adds MSMSulc surface registration, and enables it by default. To
disable it, the `--no-msm` flag has been added, and behaves similar to
`--no-fs-reconall`.
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CIFTI / Grayordinates effort: medium Estimated medium effort task feature impact: medium Estimated medium impact task
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Milestone
23.x
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ENH: Add MSMSulc nipreps/fmriprep
ENH: Add MSMSulc nipreps/fmriprep
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@effigies