diff --git a/aslprep/workflows/asl/fit.py b/aslprep/workflows/asl/fit.py index cb73704ba..b734eb4d6 100644 --- a/aslprep/workflows/asl/fit.py +++ b/aslprep/workflows/asl/fit.py @@ -21,6 +21,7 @@ # https://www.nipreps.org/community/licensing/ # """Fit workflows for ASLPrep.""" +import os import typing as ty import bids @@ -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) diff --git a/aslprep/workflows/asl/resampling.py b/aslprep/workflows/asl/resampling.py index 71e0dcc2b..7cbf1192d 100644 --- a/aslprep/workflows/asl/resampling.py +++ b/aslprep/workflows/asl/resampling.py @@ -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: @@ -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