ENH: Add option to exclude projecting high variance voxels to surface #278
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…ing Workbench interfaces
…pler option (to be continued in a separate branch)
…urfaces for test sub)
Removed duplicate code by abstracting it into functions, clarifying the goodvoxels logic
- Implemented the formatting suggestions by Mathias at the URLs below:
- nipreps#235
- nipreps/fmriprep#2855
- Split the 3 workflow-connect blocks in the project-goodvoxels section of resampling.py into 3 different functions: ribbon, outliers, and vol-to-surf
- Incomplete comments in resampling.py
Reorganized/cleaned goodvoxels resampling.py
… into madisoth-goodvoxels
remove doctests
…into nipreps_master
--- docstring update (+4 squashed commit) Squashed commit: [2493e8c] remove CreateSignedDistanceVolume doctest for now (needs anatomical surfaces for test sub) [568191c] docstring and style fixes [b14cf08] additional work on --project-goodvoxels, revert work on --surface-sampler option (to be continued in a separate branch) [42481ea] add options "--project-goodvoxels", "--surface-sampler", plus supporting Workbench interfaces
FIX: Minor anat wf & workbench.py fixes (+5 squashed commit) Squashed commit: [e995ec4] RF: Moved ribbon wf (from bold to anat) and reformatted [9676f14] Updated Docker version tag [532875e] STY: black and isort [946dc7e] Formatting fixes and resampling.py modularization - Implemented the formatting suggestions by Mathias at the URLs below: - nipreps#235 - nipreps/fmriprep#2855 - Split the 3 workflow-connect blocks in the project-goodvoxels section of resampling.py into 3 different functions: ribbon, outliers, and vol-to-surf - Incomplete comments in resampling.py [114f982] Modularized goodvoxels code in resampling.py Removed duplicate code by abstracting it into functions, clarifying the goodvoxels logic
…adisoth/nibabies into enh/project-goodvoxels-new
…erage is requested
|
@madisoth this is now completing without errors - as a final check, could you verify the outputs are as expected? |
mgxd
changed the title
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Adds option --project-goodvoxels to address nipreps/fmriprep#2822.
If enabled, voxels whose timeseries have locally high coefficient of variation, or which lie outside the cortex (based on signed distance volumes generated from the WM and pial surfaces), are excluded from volume-to-surface sampling of BOLD timeseries. Not enabled by default.