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DOC: Small updates to fix doc builds
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@effigies
effigies committed Oct 14, 2023
1 parent e3b4feb commit 3308813
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5 changes: 4 additions & 1 deletion docs/workflows.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -80,6 +80,8 @@ single reference template (see `Longitudinal processing`_).
skull_strip_fixed_seed=False,
t1w=['sub-01/anat/sub-01_T1w.nii.gz'],
t2w=[],
msm_sulc=True,
precomputed={},
)

.. important::
Expand Down Expand Up @@ -266,7 +268,8 @@ packages, including FreeSurfer and the `Connectome Workbench`_.

from smriprep.workflows.surfaces import init_surface_recon_wf
wf = init_surface_recon_wf(omp_nthreads=1,
hires=True)
hires=True,
precomputed={})

See also *sMRIPrep*'s
:py:func:`~smriprep.workflows.surfaces.init_surface_recon_wf`
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107 changes: 2 additions & 105 deletions fmriprep/workflows/bold/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -440,7 +440,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
if os.path.isfile(ref_file):
bold_tlen, mem_gb = _create_mem_gb(ref_file)

wf_name = _get_wf_name(ref_file)
wf_name = _get_wf_name(ref_file, "func_preproc")
config.loggers.workflow.debug(
"Creating bold processing workflow for <%s> (%.2f GB / %d TRs). "
"Memory resampled/largemem=%.2f/%.2f GB.",
Expand Down Expand Up @@ -605,7 +605,7 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):

summary = pe.Node(
FunctionalSummary(
slice_timing=run_stc,
# slice_timing=run_stc,
registration=("FSL", "FreeSurfer")[freesurfer],
registration_dof=config.workflow.bold2t1w_dof,
registration_init=config.workflow.bold2t1w_init,
Expand Down Expand Up @@ -790,109 +790,6 @@ def init_func_preproc_wf(bold_file, has_fieldmap=False):
)
final_boldref_wf.__desc__ = None # Unset description to avoid second appearance

# MAIN WORKFLOW STRUCTURE #######################################################
# fmt:off
workflow.connect([
# Prepare masked T1w image
(inputnode, t1w_brain, [("t1w_preproc", "in_file"),
("t1w_mask", "in_mask")]),
# Select validated bold files per-echo
(initial_boldref_wf, select_bold, [("outputnode.all_bold_files", "inlist")]),
# BOLD buffer has slice-time corrected if it was run, original otherwise
(boldbuffer, bold_split, [("bold_file", "in_file")]),
# HMC
(initial_boldref_wf, bold_hmc_wf, [
("outputnode.raw_ref_image", "inputnode.raw_ref_image"),
("outputnode.bold_file", "inputnode.bold_file"),
]),
(bold_hmc_wf, outputnode, [
("outputnode.xforms", "hmc_xforms"),
]),
# EPI-T1w registration workflow
(inputnode, bold_reg_wf, [
("t1w_dseg", "inputnode.t1w_dseg"),
# Undefined if --fs-no-reconall, but this is safe
("subjects_dir", "inputnode.subjects_dir"),
("subject_id", "inputnode.subject_id"),
("fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm"),
]),
(bold_final, bold_reg_wf, [
("boldref", "inputnode.ref_bold_brain")]),
(t1w_brain, bold_reg_wf, [("out_file", "inputnode.t1w_brain")]),
(inputnode, bold_t1_trans_wf, [
("bold_file", "inputnode.name_source"),
("t1w_mask", "inputnode.t1w_mask"),
("t1w_aseg", "inputnode.t1w_aseg"),
("t1w_aparc", "inputnode.t1w_aparc"),
]),
(t1w_brain, bold_t1_trans_wf, [("out_file", "inputnode.t1w_brain")]),
(bold_reg_wf, outputnode, [
("outputnode.itk_bold_to_t1", "bold2anat_xfm"),
("outputnode.itk_t1_to_bold", "anat2bold_xfm"),
]),
(bold_reg_wf, bold_t1_trans_wf, [
("outputnode.itk_bold_to_t1", "inputnode.itk_bold_to_t1"),
]),
(bold_final, bold_t1_trans_wf, [
("mask", "inputnode.ref_bold_mask"),
("boldref", "inputnode.ref_bold_brain"),
]),
(bold_t1_trans_wf, outputnode, [
("outputnode.bold_t1", "bold_t1"),
("outputnode.bold_t1_ref", "bold_t1_ref"),
("outputnode.bold_aseg_t1", "bold_aseg_t1"),
("outputnode.bold_aparc_t1", "bold_aparc_t1"),
]),
# Connect bold_confounds_wf
(inputnode, bold_confounds_wf, [
("t1w_tpms", "inputnode.t1w_tpms"),
("t1w_mask", "inputnode.t1w_mask"),
]),
(bold_hmc_wf, bold_confounds_wf, [
("outputnode.movpar_file", "inputnode.movpar_file"),
("outputnode.rmsd_file", "inputnode.rmsd_file"),
]),
(bold_reg_wf, bold_confounds_wf, [
("outputnode.itk_t1_to_bold", "inputnode.t1_bold_xform")
]),
(initial_boldref_wf, bold_confounds_wf, [
("outputnode.skip_vols", "inputnode.skip_vols"),
]),
(initial_boldref_wf, final_boldref_wf, [
("outputnode.skip_vols", "inputnode.dummy_scans"),
]),
(final_boldref_wf, bold_final, [
("outputnode.ref_image", "boldref"),
("outputnode.bold_mask", "mask"),
]),
(bold_final, bold_confounds_wf, [
("bold", "inputnode.bold"),
("mask", "inputnode.bold_mask"),
]),
(bold_confounds_wf, outputnode, [
("outputnode.confounds_file", "confounds"),
("outputnode.confounds_metadata", "confounds_metadata"),
("outputnode.acompcor_masks", "acompcor_masks"),
("outputnode.tcompcor_mask", "tcompcor_mask"),
]),
# Native-space BOLD files (if calculated)
(bold_final, outputnode, [
("bold", "bold_native"),
("boldref", "bold_native_ref"),
("mask", "bold_mask_native"),
("bold_echos", "bold_echos_native"),
("t2star", "t2star_bold"),
]),
# Summary
(initial_boldref_wf, summary, [("outputnode.algo_dummy_scans", "algo_dummy_scans")]),
(bold_reg_wf, summary, [("outputnode.fallback", "fallback")]),
(outputnode, summary, [("confounds", "confounds_file")]),
# Select echo indices for original/validated BOLD files
(echo_index, bold_source, [("echoidx", "index")]),
(echo_index, select_bold, [("echoidx", "index")]),
])
# fmt:on

# for standard EPI data, pass along correct file
if not multiecho:
# fmt:off
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