Merge pull request #9 from mnoergaard/main

Refactor fMRIPrep to PETPrep

Author: mnoergaard

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"""

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)
 

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 = {}

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):