ENH: uodate fmriprep to petprep

Author: mnoergaard

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):