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Fix fMRIPrep-related bugs #366

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merged 2 commits into from
Dec 8, 2023
Merged

Fix fMRIPrep-related bugs #366

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aba04bd
Fix CIFTI density bug.
tsalo Dec 8, 2023
a80e021
Ignore sbrefs when requested.
tsalo Dec 8, 2023
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9 changes: 9 additions & 0 deletions aslprep/workflows/asl/fit.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@
# https://www.nipreps.org/community/licensing/
#
"""Fit workflows for ASLPrep."""
import os
import typing as ty

import bids
Expand Down Expand Up @@ -201,6 +202,14 @@ def init_asl_fit_wf(
entity_overrides=config.execution.get().get("bids_filters", {}).get("sbref", {}),
layout=layout,
)
basename = os.path.basename(asl_file)
sbref_msg = f"No single-band-reference found for {basename}."
if sbref_file and "sbref" in config.workflow.ignore:
sbref_msg = f"Single-band reference file(s) found for {basename} and ignored."
sbref_file = []
elif sbref_file:
sbref_msg = f"Using single-band reference file(s) {os.path.basename(sbref_file)}."
config.loggers.workflow.info(sbref_msg)

# Get metadata from ASL file(s)
metadata = layout.get_metadata(asl_file)
Expand Down
7 changes: 5 additions & 2 deletions aslprep/workflows/asl/resampling.py
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Original file line number Diff line number Diff line change
Expand Up @@ -295,6 +295,9 @@ def init_bold_fsLR_resampling_wf( # noqa: N802
):
"""Resample BOLD time series to fsLR surface.

This is copied from fMRIPrep and can be replaced with an fMRIPrep import once 23.2.0 is
released.

This workflow is derived heavily from three scripts within the DCAN-HCP pipelines scripts

Line numbers correspond to the locations of the code in the original scripts, found at:
Expand Down Expand Up @@ -426,8 +429,8 @@ def init_bold_fsLR_resampling_wf( # noqa: N802
]
atlases = smriprep_data.load_resource("atlases")
select_surfaces.inputs.template_roi = [
str(atlases / "L.atlasroi.32k_fs_LR.shape.gii"),
str(atlases / "R.atlasroi.32k_fs_LR.shape.gii"),
str(atlases / f"L.atlasroi.{fslr_density}_fs_LR.shape.gii"),
str(atlases / f"R.atlasroi.{fslr_density}_fs_LR.shape.gii"),
]

# RibbonVolumeToSurfaceMapping.sh
Expand Down
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