ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011

effigies · 2023-05-18T12:31:26Z

Changes proposed in this pull request

Remove goodvoxels and CIFTI-specific code from mri_vol2surf resampling workflow. fsnative and fsaverage will remain the same for now.
Removes fsaverage as an implicit resampling target for --cifti-output. fsaverage and fsLR are now entirely independent.
Create a subject-specific cortical ROI mask in GIFTI space. Not currently output, as it's only needed internally; it's not a great mask but is intended to be more liberal than the fsLR mask applied later.
Adds a number of wb_command commands, including an OpenMP mixin that allows OMP_NUM_THREADS to be set in the environment. I think most commands can take advantage, but I only tagged slow ones (take >10s) that I could verify actually used them.
Depends on ENH: Project fsLR mesh onto native sphere to enable single-shot resampling into fsLR smriprep#339 and FIX: Move from smoothwm to white niworkflows#806.

TODO:

Restore literate workflow code.
Restore saving goodvoxels mask, if desired.

Documentation that should be reviewed

TODO

Closes #2990.

Resample, mask, fill-holes, remove-islands

…encies

…ests

effigies · 2023-06-05T17:35:11Z

@mgxd I just realized this hasn't been reviewed. Any chance you could have a look? I'll work on knocking off those two checklist points above.

mgxd

Looks good, skimmed through and nothing jumps out.

One note - the more that this can be upstreamed, the better - since we'll be using them in nibabies as well.

mgxd · 2023-06-05T17:56:29Z

fmriprep/workflows/bold/base.py

@@ -437,7 +433,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
        bids_root=layout.root,
        cifti_output=config.workflow.cifti_output,
        freesurfer=freesurfer,
-        project_goodvoxels=project_goodvoxels,
+        project_goodvoxels=False,


Just noting we should still output the ribbon mask

fmriprep/workflows/bold/resampling.py

mgxd · 2023-06-05T18:16:47Z

fmriprep/workflows/bold/resampling.py

            (goodvoxels_ribbon_mask, outputnode, [("out_file", "goodvoxels_ribbon")]),
        ]
    )

    return workflow


+def init_bold_fsLR_resampling_wf(


this is a really nice digestion of the wb commands used

effigies · 2023-06-06T19:35:46Z

One note - the more that this can be upstreamed, the better - since we'll be using them in nibabies as well.

@mgxd Do you mean push interfaces into niworkflows?

mgxd · 2023-06-06T19:56:18Z

Yes, but it was not to say that should hold this up - we can port it over for 1.8.1, cut a nwf release, and then remove it from here.

23.1.0 (June 12, 2023) New feature release in the 23.1.x series. This release substantially reworks the resampling to fsLR grayordinate space, better accounting for partial volumes and high variance voxels. If you are resampling using ``--project-goodvoxels``, we strongly recommend upgrading. Fieldmap handling is improved, with better preference given to single-band references in both PEPolar and SyN-SDC schemes. Additionally, fMRIPrep will no longer estimate fieldmaps that are not intended to be used to correct BOLD series, reducing unneeded processing. This release removes ICA-AROMA from the fMRIPrep workflow. To use ICA-AROMA, set ``MNI152NLin6Asym:res-2`` as a target output space. MELODIC and ICA-AROMA can be run on the resulting images in a separate pipeline. For further information on the reasoning behind this change, see `GitHub issue #2936 <https://github.com/nipreps/fmriprep/issues/2936>`__. This release increments the versions of ANTs and FSL bundled in the Docker image. With thanks to Eilidh MacNicol, Basille Pinsard and Taylor Salo for contributions in fMRIPrep and SDCflows. * FIX: Raise RuntimeError at build if echos have mismatched shapes (#3028) * FIX: Inconsistent fmapless estimation when ignoring fieldmaps (#2994) * FIX: Dilate BOLD mask by 2 voxels to prevent over-aggressive masking degrading T2* map estimation (#2986) * FIX: Estimate free memory with "available", not "free" (#2985) * ENH: Add ``--me-t2s-fit-method`` parameter (#3030) * ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate (#3011) * ENH: Allow SBref+EPI PEPolar fieldmaps to correct BOLD series (#3008) * ENH: Remove ICA-AROMA from workflow and docs (#2966) * RF: Filter fieldmaps based on whether they will be used to correct a BOLD series (#3025) * MNT: Update ANTs pin in Docker image (#3016) * MNT: Update governance docs (#2992) * MNT: Refactor Docker build process (#2982) * MNT: Pin conda environment more strictly (#2853) * MNT: Require niworkflows ~1.3.6 (#2740) * CI: Use registry for layer caching (#3012) * CI: Upgrade docker orb (#2865)

feilong · 2023-07-20T17:17:31Z

fmriprep/workflows/bold/resampling.py

+            from fmriprep.workflows.bold.resampling import init_bold_fsLR_resampling_wf
+            wf = init_bold_fsLR_resampling_wf(
+                estimate_goodvoxels=True,
+                grayord_density='92k',


Perhaps grayord_density='91k' instead of 92k based on the Parameters below?

effigies force-pushed the fix/goodvoxels branch 3 times, most recently from dbb09fa to 2accbd2 Compare May 18, 2023 18:40

effigies mentioned this pull request May 19, 2023

FIX: Mask BOLD with goodvoxels, not goodvoxels+ribbon #2998

Closed

madisoth mentioned this pull request May 23, 2023

autorecon1 "ERROR: OS is missing bc (binary calculator) utility" #3015

Closed

effigies force-pushed the fix/goodvoxels branch from 6762be9 to d50177d Compare May 24, 2023 01:58

This was referenced Jun 2, 2023

FIX: Update sloppy/debug parameters in anatomical base workflow #3022

Closed

REL: 0.12.0 nipreps/smriprep#345

Merged

effigies and others added 14 commits June 2, 2023 16:08

MNT: Pin master branches of nipreps dependencies

02e51c5

ENH: Add several workbench commands

70b93b9

Resample, mask, fill-holes, remove-islands

ENH: Add GIFTI interface to generate ROI from thickness

972648a

ENH: Add fsLR resampling workflow

90621c2

RF: Remove goodvoxels from mri_vol2surf workflow

4d03abf

RF: Remove implicit fsaverage resampling from --cifti-output

9508e86

RF: Remove cifti dependency on fsaverage workflow

c2f4aff

ENH: Add OpenMPCommandMixin to enable n_procs

21e5c3b

DOCKER: Re-add git to main image to enable installing unstable depend…

7a42c27

…encies

TEST: Copy test data folder and cd to temp path during interface doct…

e071a4e

…ests

FIX: Sort surfaces by basename, not full path

297d78e

DOCTEST: Explicit normalize_whitespace for --pyargs friendliness

68b6140

FIX: Update sloppy/debug parameters in anatomical base workflow

47c7b28

CI: Update expected outputs

64eecd6

effigies force-pushed the fix/goodvoxels branch from f1ac994 to 64eecd6 Compare June 2, 2023 20:11

effigies requested a review from mgxd June 5, 2023 17:34

Cleanup old comments and disjointed workflow connections

a247fc2

mgxd reviewed Jun 5, 2023

View reviewed changes

effigies added 3 commits June 5, 2023 16:30

REPORT: Restore goodvoxels reporting, with slight clarification

606ed37

ENH: Output goodvoxels mask (not constrained to ribbon)

926a03b

DOC: Update docs and workflow docstring

ee3ebc2

effigies force-pushed the fix/goodvoxels branch from 9556568 to ee3ebc2 Compare June 5, 2023 20:30

effigies added 3 commits June 5, 2023 16:45

DOC: Clean up Sphinx warnings

63092fd

FIX: Separate joinnode from outputnode

6e4e50e

CI: Expect goodvoxels mask

3a3d9b4

effigies merged commit c56bec6 into nipreps:master Jun 6, 2023

mgxd mentioned this pull request Jun 7, 2023

ENH: Port GIFTI/CIFTI interfaces from fMRIPrep nipreps/niworkflows#811

Merged

mgxd mentioned this pull request Jun 21, 2023

FIX: "Goodvoxels" projection nipreps/nibabies#300

Merged

Shotgunosine mentioned this pull request Jun 22, 2023

Documentation for init_bold_grayords_wf out of date #3050

Closed

feilong reviewed Jul 20, 2023

View reviewed changes

effigies deleted the fix/goodvoxels branch August 24, 2023 03:42

tsalo mentioned this pull request Dec 4, 2023

Goodvoxels mask no longer written out in 23.2.0a2 #3168

Closed

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ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011

ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011

effigies commented May 18, 2023 •

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effigies commented Jun 5, 2023

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effigies commented Jun 6, 2023 •

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mgxd commented Jun 6, 2023

feilong Jul 20, 2023

ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011

ENH: Resample BOLD to fsLR directly, dropping fsaverage intermediate #3011

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effigies commented May 18, 2023 • edited Loading

Changes proposed in this pull request

Documentation that should be reviewed

effigies commented Jun 5, 2023

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