ENH: Add Multimodal Surface Matching

[mgxd]

Closes #353.

[codecov]

Codecov Report

Patch coverage: 65.97% and project coverage change: -20.37% ⚠️

Comparison is base (5e60fd8) 54.03% compared to head (536cfb4) 33.67%.
Report is 2 commits behind head on master.

Additional details and impacted files

@@             Coverage Diff             @@
##           master     #358       +/-   ##
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- Coverage   54.03%   33.67%   -20.37%     
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  Files          22       21        -1     
  Lines        1488     1574       +86     
  Branches      209      212        +3     
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- Hits          804      530      -274     
- Misses        628     1029      +401     
+ Partials       56       15       -41     

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Files Changed	Coverage Δ
smriprep/cli/run.py	2.80% <0.00%> (-71.38%)	⬇️
smriprep/workflows/anatomical.py	16.56% <0.00%> (-29.00%)	⬇️
smriprep/workflows/base.py	30.00% <ø> (-41.67%)	⬇️
smriprep/workflows/surfaces.py	11.57% <11.53%> (-0.33%)	⬇️
smriprep/interfaces/msm.py	76.47% <76.47%> (ø)
smriprep/__about__.py	100.00% <100.00%> (ø)
smriprep/interfaces/workbench.py	100.00% <100.00%> (ø)

... and 8 files with indirect coverage changes

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[effigies]

I'm able to follow this so far. Is there more to go, or was the FNIRT stuff a red herring?

[mgxd]

No, it looks like those are still to come (see below), though I'm not sure if it should be included here or in a separate PR.

Steps

 # 4) Apply T1w-to-MNI affine and warpfield xfms (XCP-D)??
    # wb_command -surface-apply-affine \
    # /wkdir/xcpd_wf/single_subject_${SUB}_wf/postprocess_surfaces_wf/warp_surfaces_to_template_wf/lh_apply_transforms_wf/resample_to_fsLR32k/mapflow/_resample_to_fsLR32k0/resampled_sub-${SUB}_ses-${SES}_hemi-L_pial.surf.gii \
    # /wkdir/xcpd_wf/single_subject_${SUB}_wf/postprocess_surfaces_wf/warp_surfaces_to_template_wf/update_xfm_wf/convert_xfm2world/00_T1w_to_MNI152NLin6Asym_AffineTransform_MatrixOffsetTransformBase_world.nii.gz \
    # MNIAffine_resampled_sub-{SUB}_ses-${SES}_hemi-L_pial.surf.gii
    #
    # wb_command -surface-apply-warpfield \
    # /wkdir/xcpd_wf/single_subject_${SUB}_wf/postprocess_surfaces_wf/warp_surfaces_to_template_wf/lh_apply_transforms_wf/apply_affine_to_fsLR32k/mapflow/_apply_affine_to_fsLR32k0/MNIAffine_resampled_sub-${SUB}_ses-${SES}_hemi-L_pial.surf.gii \
    # /wkdir/xcpd_wf/single_subject_${SUB}_wf/postprocess_surfaces_wf/warp_surfaces_to_template_wf/update_xfm_wf/remerge_inv_warpfield/concat_4d.nii.gz \
    # MNIwarped_MNIAffine_resampled_sub-${SUB}_ses-${SES}_hemi-L_pial.surf.gii \
    # -fnirt /wkdir/xcpd_wf/single_subject_${SUB}_wf/postprocess_surfaces_wf/warp_surfaces_to_template_wf/update_xfm_wf/remerge_warpfield/concat_4d.nii.gz
    ## /wkdir is the XCP-D (0.4.x) work directory

    ## after doing both pial and white, use wb_command -surface-average to make midthickness surfs
    ## (I then copied those midthickness surfs to /hackathon_MSM/32k_MNIaligned_msm_surfs/MNIwarped_MNIAffine_resampled_sub-${SUB}_ses-${SES}_hemi-L_midthickness.surf.gii)


    # 5) Resample morphometrics from native to 32k:
    # wb_command -metric-resample \
    # /anat/sub-${SUB}_ses-${SES}_hemi-L_curv.shape.gii /hackathon_MSM/L.sphere.reg.surf.gii  \
    # ~/.cache/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii \
    # ADAP_BARY_AREA \
    # space-fsLR_hemi-L_den-91k_curv.shape.gii \
    # -area-surfs \
    # /anat/sub-${SUB}_ses-${SES}_hemi-L_midthickness.surf.gii \
    # /hackathon_MSM/32k_MNIaligned_msm_surfs/MNIwarped_MNIAffine_resampled_sub-${SUB}_ses-${SES}_hemi-L_midthickness.surf.gii

    # 6) Resample BOLD timeseries
    # wb_command -metric-resample \
    # /wd/fmriprep_23_1_wf/single_subject_${SUB}_wf/func_preproc_ses_${SES}_task_${TASK}_run_${RUN}_echo_1_wf/bold_fsLR_resampling_wf/_hemi_L/metric_dilate/lh.midthickness_converted_mapped.func.func.gii \
    # /hackathon_MSM/L.sphere.reg.surf.gii \
    # ~/.cache/templateflow/tpl-fsLR/tpl-fsLR_hemi-L_den-32k_sphere.surf.gii \
    # ADAP_BARY_AREA \
    # /hackathon_MSM/sub-${SUB}_ses-${SES}_task-${TASK}_run-${RUN}_space-fsLR_hemi-L_den-32k_bold.func.gii \
    # -area-surfs /wd/fmriprep_23_1_wf/single_subject_${SUB}_wf/anat_preproc_wf/surface_recon_wf/gifti_surface_wf/fix_surfs/mapflow/_fix_surfs*/lh.midthickness_converted.gii \
    # /hackathon_MSM/32k_MNIaligned_msm_surfs/MNIwarped_MNIAffine_resampled_sub-${SUB}_ses-${SES}_hemi-L_midthickness.surf.gii

[effigies]

Overall LGTM

[effigies]

This LGTM. One small comment.

[effigies]

@mgxd See fe8f7ca for the merge into next. Please let me know if you see any issues.