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ENH: Restore resampling to surface GIFTIs #3126

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merged 3 commits into from
Nov 13, 2023
Merged

ENH: Restore resampling to surface GIFTIs #3126

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c4d1a00
RF: Remove datasinks already reimplemented elsewhere
effigies Nov 3, 2023
d378af3
ENH: Restore resampling to FreeSurfer surfaces
effigies Nov 3, 2023
c79464e
FIX: Moving and reference apply to the forward transform, not the final
effigies Nov 7, 2023
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41 changes: 20 additions & 21 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -442,6 +442,26 @@
(bold_std_wf, ds_bold_std_wf, [('outputnode.bold_file', 'inputnode.bold')]),
]) # fmt:skip

if config.workflow.run_reconall and freesurfer_spaces:
config.loggers.workflow.debug("Creating BOLD surface-sampling workflow.")
bold_surf_wf = init_bold_surf_wf(

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fmriprep/workflows/bold/base.py#L445-L447 

Added lines #L445 - L447 were not covered by tests
mem_gb=mem_gb["resampled"],
surface_spaces=freesurfer_spaces,
medial_surface_nan=config.workflow.medial_surface_nan,
metadata=all_metadata[0],
output_dir=fmriprep_dir,
name="bold_surf_wf",
)
bold_surf_wf.inputs.inputnode.source_file = bold_file
workflow.connect([

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fmriprep/workflows/bold/base.py#L455-L456 

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(inputnode, bold_surf_wf, [
("subjects_dir", "inputnode.subjects_dir"),
("subject_id", "inputnode.subject_id"),
("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
]),
(bold_anat_wf, bold_surf_wf, [("outputnode.bold_file", "inputnode.bold_t1w")]),
]) # fmt:skip

bold_confounds_wf = init_bold_confs_wf(
mem_gb=mem_gb["largemem"],
metadata=all_metadata[0],
Expand Down Expand Up @@ -723,27 +743,6 @@
)

# SURFACES ##################################################################################
# Freesurfer
if freesurfer and freesurfer_spaces:
config.loggers.workflow.debug("Creating BOLD surface-sampling workflow.")
bold_surf_wf = init_bold_surf_wf(
mem_gb=mem_gb["resampled"],
surface_spaces=freesurfer_spaces,
medial_surface_nan=config.workflow.medial_surface_nan,
name="bold_surf_wf",
)
# fmt:off
workflow.connect([
(inputnode, bold_surf_wf, [
("subjects_dir", "inputnode.subjects_dir"),
("subject_id", "inputnode.subject_id"),
("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
]),
(bold_t1_trans_wf, bold_surf_wf, [("outputnode.bold_t1", "inputnode.source_file")]),
(bold_surf_wf, outputnode, [("outputnode.surfaces", "surfaces")]),
(bold_surf_wf, func_derivatives_wf, [("outputnode.target", "inputnode.surf_refs")]),
])
# fmt:on

# CIFTI output
if config.workflow.cifti_output:
Expand Down