Merge pull request #4 from mnoergaard/main

Refactor of fMRIPrep to PETPrep

Author: mnoergaard

fmriprep/cli/parser.py

@@ -145,6 +145,16 @@ def _slice_time_ref(value, parser):
             raise parser.error(f'Slice time reference must be in range 0-1. Received {value}.')
         return value
 
+    def _reference_frame(value, parser):
+        if value == 'average':
+            return 'average'
+        try:
+            return int(value)
+        except ValueError:
+            raise parser.error(
+                "Reference frame must be an integer index or 'average'."
+            ) from None
+
     verstr = f'PETPrep v{config.environment.version}'
     currentv = Version(config.environment.version)
     is_release = not any((currentv.is_devrelease, currentv.is_prerelease, currentv.is_postrelease))
@@ -158,6 +168,7 @@ def _slice_time_ref(value, parser):
     IsFile = partial(_is_file, parser=parser)
     PositiveInt = partial(_min_one, parser=parser)
     BIDSFilter = partial(_bids_filter, parser=parser)
+    ReferenceFrame = partial(_reference_frame, parser=parser)
 
     # Arguments as specified by BIDS-Apps
     # required, positional arguments
@@ -377,12 +388,15 @@ def _slice_time_ref(value, parser):
         help='Deprecated - use `--force no-bbr` instead.',
     )
     g_conf.add_argument(
-        '--dummy-scans',
-        required=False,
+        '--reference-frame',
         action='store',
-        default=None,
-        type=int,
-        help='Number of nonsteady-state volumes. Overrides automatic detection.',
+        dest='reference_frame',
+        type=ReferenceFrame,
+        default='average',
+        help=(
+            "Reference frame index (0-based) for PET preprocessing. "
+            "Use 'average' to compute the standard averaged reference."
+        ),
     )
     g_conf.add_argument(
         '--random-seed',

fmriprep/config.py

@@ -556,8 +556,6 @@ class workflow(_Config):
     """Initial transform for PET-to-anatomical registration."""
     cifti_output = None
     """Generate HCP Grayordinates, accepts either ``'91k'`` (default) or ``'170k'``."""
-    dummy_scans = None
-    """Set a number of initial scans to be considered nonsteady states."""
     hires = None
     """Run FreeSurfer ``recon-all`` with the ``-hires`` flag."""
     fs_no_resume = None
@@ -594,7 +592,10 @@ class workflow(_Config):
     spaces = None
     """Keeps the :py:class:`~niworkflows.utils.spaces.SpatialReferences`
     instance keeping standard and nonstandard spaces."""
+    reference_frame: int | str | None = None
+    """Selected frame index for PET reference generation.
 
+    ``None`` or ``'average'`` retains the current averaging behavior."""
 
 class loggers:
     """Keep loggers easily accessible (see :py:func:`init`)."""

fmriprep/interfaces/confounds.py

@@ -336,9 +336,6 @@ class GatherConfoundsInputSpec(BaseInterfaceInputSpec):
     std_dvars = File(exists=True, desc='file containing standardized DVARS')
     fd = File(exists=True, desc='input framewise displacement')
     rmsd = File(exists=True, desc='input RMS framewise displacement')
-    tcompcor = File(exists=True, desc='input tCompCorr')
-    acompcor = File(exists=True, desc='input aCompCorr')
-    crowncompcor = File(exists=True, desc='input crown-based regressors')
     cos_basis = File(exists=True, desc='input cosine basis')
     motion = File(exists=True, desc='input motion parameters')
 
@@ -379,9 +376,6 @@ def _run_interface(self, runtime):
             std_dvars=self.inputs.std_dvars,
             fdisp=self.inputs.fd,
             rmsd=self.inputs.rmsd,
-            tcompcor=self.inputs.tcompcor,
-            acompcor=self.inputs.acompcor,
-            crowncompcor=self.inputs.crowncompcor,
             cos_basis=self.inputs.cos_basis,
             motion=self.inputs.motion,
             newpath=runtime.cwd,
@@ -397,9 +391,6 @@ def _gather_confounds(
     std_dvars=None,
     fdisp=None,
     rmsd=None,
-    tcompcor=None,
-    acompcor=None,
-    crowncompcor=None,
     cos_basis=None,
     motion=None,
     newpath=None,
@@ -449,9 +440,6 @@ def _adjust_indices(left_df, right_df):
         (dvars, 'DVARS'),
         (fdisp, 'Framewise displacement'),
         (rmsd, 'Framewise displacement (RMS)'),
-        (tcompcor, 'tCompCor'),
-        (acompcor, 'aCompCor'),
-        (crowncompcor, 'crownCompCor'),
         (cos_basis, 'Cosine basis'),
         (motion, 'Motion parameters'),
     ):

fmriprep/interfaces/reports.py

@@ -151,10 +151,10 @@ def _generate_segment(self):
             t2w_seg = f'(+ {len(self.inputs.t2w):d} T2-weighted)'
 
         # Add list of tasks with number of runs
-        pet_series = self.inputs.bold or []
+        pet_series = self.inputs.pet or []
 
         counts = Counter(
-            BIDS_NAME.search(series).groupdict().get('task_id', 'task-<none>')[5:]
+            (BIDS_NAME.search(series).groupdict().get('task_id') or 'task-<none>')[5:]
             for series in pet_series
         )
 

fmriprep/interfaces/tests/test_reports.py

@@ -50,3 +50,25 @@
 )
 def test_get_world_pedir(tmpdir, orientation, pe_dir, expected):
     assert get_world_pedir(orientation, pe_dir) == expected
+
+
+def test_subject_summary_handles_missing_task(tmp_path):
+    from ..reports import SubjectSummary
+
+    t1w = tmp_path / 'sub-01_T1w.nii.gz'
+    t1w.write_text('')
+    pet1 = tmp_path / 'sub-01_task-rest_run-01_pet.nii.gz'
+    pet1.write_text('')
+    pet2 = tmp_path / 'sub-01_run-01_pet.nii.gz'
+    pet2.write_text('')
+
+    summary = SubjectSummary(
+        t1w=[str(t1w)],
+        pet=[str(pet1), str(pet2)],
+        std_spaces=[],
+        nstd_spaces=[],
+    )
+
+    segment = summary._generate_segment()
+    assert 'Task: rest (1 run)' in segment
+    assert 'Task: <none> (1 run)' in segment

fmriprep/workflows/base.py

@@ -199,14 +199,20 @@ def init_single_subject_wf(subject_id: str):
 ### References
 
 """
+    from niworkflows.utils.bids import DEFAULT_BIDS_QUERIES
+    import copy
+
+    queries = copy.deepcopy(DEFAULT_BIDS_QUERIES)
+    queries['t1w'].pop('datatype', None)
 
     subject_data = collect_data(
-        config.execution.layout,
+        config.execution.bids_dir,
         subject_id,
-        task=config.execution.task_id,
         bids_filters=config.execution.bids_filters,
+        queries=queries
     )[0]
 
+
     if 'flair' in config.workflow.ignore:
         subject_data['flair'] = []
     if 't2w' in config.workflow.ignore:

fmriprep/workflows/pet/base.py

@@ -543,7 +543,6 @@ def init_pet_wf(
             ('outputnode.petref', 'inputnode.petref'),
             ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
             ('outputnode.petref2anat_xfm', 'inputnode.petref2anat_xfm'),
-            ('outputnode.dummy_scans', 'inputnode.skip_vols'),
         ]),
         (pet_native_wf, pet_confounds_wf, [
             ('outputnode.pet_native', 'inputnode.pet'),
@@ -575,7 +574,6 @@ def _last(inlist):
                 ('mni2009c2anat_xfm', 'inputnode.std2anat_xfm'),
             ]),
             (pet_fit_wf, carpetplot_wf, [
-                ('outputnode.dummy_scans', 'inputnode.dummy_scans'),
                 ('outputnode.pet_mask', 'inputnode.pet_mask'),
                 ('outputnode.petref2anat_xfm', 'inputnode.petref2anat_xfm'),
             ]),
@@ -585,7 +583,6 @@ def _last(inlist):
             (pet_confounds_wf, carpetplot_wf, [
                 ('outputnode.confounds_file', 'inputnode.confounds_file'),
                 ('outputnode.crown_mask', 'inputnode.crown_mask'),
-                (('outputnode.acompcor_masks', _last), 'inputnode.acompcor_mask'),
             ]),
         ])  # fmt:skip