diff --git a/petprep/cli/workflow.py b/petprep/cli/workflow.py index 5fd1917..6a8c6b6 100644 --- a/petprep/cli/workflow.py +++ b/petprep/cli/workflow.py @@ -38,8 +38,8 @@ def build_workflow(config_file, retval): from niworkflows.utils.bids import collect_participants from niworkflows.utils.misc import check_valid_fs_license - from fmriprep.reports.core import generate_reports - from fmriprep.utils.bids import check_pipeline_version + from petprep.reports.core import generate_reports + from petprep.utils.bids import check_pipeline_version from .. import config, data from ..utils.misc import check_deps @@ -54,18 +54,18 @@ def build_workflow(config_file, retval): retval['return_code'] = 1 retval['workflow'] = None - banner = [f'Running fMRIPrep version {version}'] + banner = [f'Running PETPrep version {version}'] notice_path = data.load.readable('NOTICE') if notice_path.exists(): banner[0] += '\n' banner += [f'License NOTICE {"#" * 50}'] - banner += [f'fMRIPrep {version}'] + banner += [f'PETPrep {version}'] banner += notice_path.read_text().splitlines(keepends=False)[1:] banner += ['#' * len(banner[1])] build_log.log(25, f'\n{" " * 9}'.join(banner)) # warn if older results exist: check for dataset_description.json in output folder - msg = check_pipeline_version('fMRIPrep', version, petprep_dir / 'dataset_description.json') + msg = check_pipeline_version('PETPrep', version, petprep_dir / 'dataset_description.json') if msg is not None: build_log.warning(msg) @@ -108,7 +108,7 @@ def build_workflow(config_file, retval): # Build main workflow init_msg = [ - "Building fMRIPrep's workflow:", + "Building PETPrep's workflow:", f'BIDS dataset path: {config.execution.bids_dir}.', f'Participant list: {subject_list}.', f'Run identifier: {config.execution.run_uuid}.', @@ -133,13 +133,13 @@ def build_workflow(config_file, retval): build_log.critical( """\ ERROR: Federal Information Processing Standard (FIPS) mode is enabled on your system. \ -FreeSurfer (and thus fMRIPrep) cannot be used in FIPS mode. \ +FreeSurfer (and thus PETPrep) cannot be used in FIPS mode. \ Contact your system administrator for assistance.""" ) else: build_log.critical( """\ -ERROR: a valid license file is required for FreeSurfer to run. fMRIPrep looked for an existing \ +ERROR: a valid license file is required for FreeSurfer to run. PETPrep looked for an existing \ license file at several paths, in this order: 1) command line argument ``--fs-license-file``; \ 2) ``$FS_LICENSE`` environment variable; and 3) the ``$FREESURFER_HOME/license.txt`` path. Get it \ (for free) by registering at https://surfer.nmr.mgh.harvard.edu/registration.html""" diff --git a/petprep/workflows/base.py b/petprep/workflows/base.py index 150ca8b..19538b0 100644 --- a/petprep/workflows/base.py +++ b/petprep/workflows/base.py @@ -21,7 +21,7 @@ # https://www.nipreps.org/community/licensing/ # """ -fMRIPrep base processing workflows +PETPrep base processing workflows ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ .. autofunction:: init_fmriprep_wf @@ -166,12 +166,12 @@ def init_single_subject_wf(subject_id: str): init_resample_surfaces_wf, ) - from fmriprep.workflows.pet.base import init_pet_wf + from petprep.workflows.pet.base import init_pet_wf workflow = Workflow(name=f'sub_{subject_id}_wf') workflow.__desc__ = f""" Results included in this manuscript come from preprocessing -performed using *fMRIPrep* {config.environment.version} +performed using *PETPrep* {config.environment.version} (@fmriprep1; @fmriprep2; RRID:SCR_016216), which is based on *Nipype* {config.environment.nipype_version} (@nipype1; @nipype2; RRID:SCR_002502). @@ -544,7 +544,7 @@ def init_single_subject_wf(subject_id: str): for pet_series in pet_runs: pet_cache = {} if config.execution.derivatives: - from fmriprep.utils.bids import collect_derivatives, extract_entities + from petprep.utils.bids import collect_derivatives, extract_entities entities = extract_entities(pet_series) diff --git a/petprep/workflows/pet/fit.py b/petprep/workflows/pet/fit.py index 20efc3b..b06360e 100644 --- a/petprep/workflows/pet/fit.py +++ b/petprep/workflows/pet/fit.py @@ -122,7 +122,7 @@ def init_pet_fit_wf( """ from niworkflows.engine.workflows import LiterateWorkflow as Workflow - from fmriprep.utils.misc import estimate_pet_mem_usage + from petprep.utils.misc import estimate_pet_mem_usage if precomputed is None: precomputed = {} diff --git a/petprep/workflows/pet/outputs.py b/petprep/workflows/pet/outputs.py index d2c3b51..04d9786 100644 --- a/petprep/workflows/pet/outputs.py +++ b/petprep/workflows/pet/outputs.py @@ -30,10 +30,10 @@ from niworkflows.interfaces.fixes import FixHeaderApplyTransforms as ApplyTransforms from niworkflows.utils.images import dseg_label -from fmriprep import config -from fmriprep.config import DEFAULT_MEMORY_MIN_GB -from fmriprep.interfaces import DerivativesDataSink -from fmriprep.interfaces.bids import BIDSURI +from petprep import config +from petprep.config import DEFAULT_MEMORY_MIN_GB +from petprep.interfaces import DerivativesDataSink +from petprep.interfaces.bids import BIDSURI def prepare_timing_parameters(metadata: dict):