FIX: remove dummy scans

Author: mnoergaard

fmriprep/cli/parser.py

@@ -387,14 +387,6 @@ def _reference_frame(value, parser):
         action=DeprecatedAction,
         help='Deprecated - use `--force no-bbr` instead.',
     )
-    g_conf.add_argument(
-        '--dummy-scans',
-        required=False,
-        action='store',
-        default=None,
-        type=int,
-        help='Number of nonsteady-state volumes. Overrides automatic detection.',
-    )
     g_conf.add_argument(
         '--reference-frame',
         action='store',

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

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'),
             ]),

fmriprep/workflows/pet/confounds.py

@@ -121,8 +121,6 @@ def init_pet_confs_wf(
         PET series mask
     motion_xfm
         ITK-formatted head motion transforms
-    skip_vols
-        number of non steady state volumes
     t1w_mask
         Mask of the skull-stripped template image
     t1w_tpms
@@ -214,7 +212,6 @@ def init_pet_confs_wf(
                 'pet_mask',
                 'petref',
                 'motion_xfm',
-                'skip_vols',
                 't1w_mask',
                 't1w_tpms',
                 'petref2anat_xfm',
@@ -398,7 +395,6 @@ def _select_cols(table):
         # Set outputs
         (spike_regress, outputnode, [('confounds_file', 'confounds_file')]),
         (mrg_conf_metadata2, outputnode, [('out_dict', 'confounds_metadata')]),
-        (inputnode, conf_corr_plot, [('skip_vols', 'ignore_initial_volumes')]),
         (concat, conf_corr_plot, [('confounds_file', 'confounds_file'),
                                   (('confounds_file', _select_cols), 'columns')]),
         (conf_corr_plot, ds_report_conf_corr, [('out_file', 'in_file')]),
@@ -445,8 +441,6 @@ def init_carpetplot_wf(
         PET image in CIFTI format, to be used in place of volumetric PET
     crown_mask
         Mask of brain edge voxels
-    dummy_scans
-        Number of nonsteady states to be dropped at the beginning of the timeseries.
 
     Outputs
     -------
@@ -467,7 +461,6 @@ def init_carpetplot_wf(
                 'std2anat_xfm',
                 'cifti_pet',
                 'crown_mask',
-                'dummy_scans',
             ]
         ),
         name='inputnode',
@@ -546,7 +539,6 @@ def init_carpetplot_wf(
         (inputnode, conf_plot, [
             ('pet', 'in_nifti'),
             ('confounds_file', 'confounds_file'),
-            ('dummy_scans', 'drop_trs'),
         ]),
         (mrg_xfms, resample_parc, [('out', 'transforms')]),
         (resample_parc, parcels, [('output_image', 'segmentation')]),

fmriprep/workflows/pet/fit.py

@@ -41,7 +41,7 @@
     init_func_fit_reports_wf,
     prepare_timing_parameters,
 )
-from .reference import init_raw_petref_wf, init_validation_and_dummies_wf
+from .reference import init_raw_petref_wf
 from .registration import init_pet_reg_wf
 
 
@@ -107,8 +107,6 @@ def init_pet_fit_wf(
     petref2anat_xfm
         Affine transform mapping from PET reference space to the anatomical
         space.
-    dummy_scans
-        The number of dummy scans declared or detected at the beginning of the series.
 
     See Also
     --------
@@ -165,7 +163,6 @@ def init_pet_fit_wf(
     outputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
-                'dummy_scans',
                 'petref',
                 'pet_mask',
                 'motion_xfm',
@@ -255,6 +252,7 @@ def init_pet_fit_wf(
             pet_file=pet_file,
             reference_frame=config.workflow.reference_frame,
         )
+        petref_wf.inputs.inputnode.dummy_scans = config.workflow.dummy_scans
 
         ds_petref_wf = init_ds_petref_wf(
             bids_root=layout.root,
@@ -268,7 +266,6 @@ def init_pet_fit_wf(
             (petref_wf, petref_buffer, [
                 ('outputnode.pet_file', 'pet_file'),
                 ('outputnode.petref', 'petref'),
-                ('outputnode.skip_vols', 'dummy_scans'),
             ]),
             (petref_buffer, ds_petref_wf, [('petref', 'inputnode.petref')]),
             (petref_wf, func_fit_reports_wf, [
@@ -281,18 +278,14 @@ def init_pet_fit_wf(
     else:
         config.loggers.workflow.info('Found HMC petref - skipping Stage 1')
 
-        validation_and_dummies_wf = init_validation_and_dummies_wf(pet_file=pet_file)
+        val_pet = pe.Node(ValidateImage(), name='val_pet')
 
         workflow.connect([
-            (validation_and_dummies_wf, petref_buffer, [
-                ('outputnode.pet_file', 'pet_file'),
-                ('outputnode.skip_vols', 'dummy_scans'),
-            ]),
-            (validation_and_dummies_wf, func_fit_reports_wf, [
-                ('outputnode.validation_report', 'inputnode.validation_report'),
-            ]),
+            (val_pet, petref_buffer, [('out_file', 'pet_file')]),
+            (val_pet, func_fit_reports_wf, [('out_report', 'inputnode.validation_report')]),
             (petref_buffer, petref_source_buffer, [('petref', 'in_file')]),
         ])  # fmt:skip
+        val_pet.inputs.in_file = pet_file
 
     # Stage 2: Estimate head motion
     if not hmc_xforms:
@@ -415,8 +408,6 @@ def init_pet_native_wf(
 
     _, mem_gb = estimate_pet_mem_usage(pet_file)
 
-    run_stc = bool(metadata.get('SliceTiming')) and 'slicetiming' not in config.workflow.ignore
-
     workflow = pe.Workflow(name=name)
 
     inputnode = pe.Node(
@@ -426,7 +417,6 @@ def init_pet_native_wf(
                 'petref',
                 'pet_mask',
                 'motion_xfm',
-                'dummy_scans',
             ],
         ),
         name='inputnode',

fmriprep/workflows/pet/reference.py

@@ -24,7 +24,6 @@
 from nipype.pipeline import engine as pe
 from niworkflows.engine.workflows import LiterateWorkflow as Workflow
 from niworkflows.interfaces.header import ValidateImage
-from niworkflows.utils.misc import pass_dummy_scans
 from nipype.interfaces import fsl
 
 DEFAULT_MEMORY_MIN_GB = 0.01
@@ -67,20 +66,13 @@ def init_raw_petref_wf(
     ------
     pet_file : str
         PET series NIfTI file
-    dummy_scans : int or None
-        Number of non-steady-state volumes specified by user at beginning of ``pet_file``
 
     Outputs
     -------
     pet_file : str
         Validated PET series NIfTI file
     petref : str
         Reference image to which PET series is motion corrected
-    skip_vols : int
-        Number of non-steady-state volumes selected at beginning of ``pet_file``
-    algo_dummy_scans : int
-        Number of non-steady-state volumes agorithmically detected at
-        beginning of ``pet_file``
 
     """
     from niworkflows.interfaces.images import RobustAverage
@@ -92,16 +84,14 @@ def init_raw_petref_wf(
 """
 
     inputnode = pe.Node(
-        niu.IdentityInterface(fields=['pet_file', 'dummy_scans']),
+        niu.IdentityInterface(fields=['pet_file']),
         name='inputnode',
     )
     outputnode = pe.Node(
         niu.IdentityInterface(
             fields=[
                 'pet_file',
                 'petref',
-                'skip_vols',
-                'algo_dummy_scans',
                 'validation_report',
             ]
         ),
@@ -112,7 +102,7 @@ def init_raw_petref_wf(
     if pet_file is not None:
         inputnode.inputs.pet_file = pet_file
 
-    validation_and_dummies_wf = init_validation_and_dummies_wf()
+    val_pet = pe.Node(ValidateImage(), name='val_pet', mem_gb=DEFAULT_MEMORY_MIN_GB)
 
     gen_avg = pe.Node(RobustAverage(), name='gen_avg', mem_gb=1)
     extract_roi = pe.Node(
@@ -123,34 +113,26 @@ def init_raw_petref_wf(
 
     workflow.connect(
         [
-            (inputnode, validation_and_dummies_wf, [
-                ('pet_file', 'inputnode.pet_file'),
-                ('dummy_scans', 'inputnode.dummy_scans'),
-            ]),
-            (validation_and_dummies_wf, outputnode, [
-                ('outputnode.pet_file', 'pet_file'),
-                ('outputnode.skip_vols', 'skip_vols'),
-                ('outputnode.algo_dummy_scans', 'algo_dummy_scans'),
-                ('outputnode.validation_report', 'validation_report'),
+            (inputnode, val_pet, [('pet_file', 'in_file')]),
+            (val_pet, outputnode, [
+                ('out_file', 'pet_file'),
+                ('out_report', 'validation_report'),
             ]),
         ]
     )  # fmt:skip
 
     if reference_frame in (None, 'average'):
         workflow.connect(
             [
-                (validation_and_dummies_wf, gen_avg, [
-                    ('outputnode.pet_file', 'in_file'),
-                    ('outputnode.t_mask', 't_mask'),
-                ]),
+                (val_pet, gen_avg, [('out_file', 'in_file')]),
                 (gen_avg, outputnode, [('out_file', 'petref')]),
             ]
         )  # fmt:skip
     else:
         extract_roi.inputs.t_min = int(reference_frame)
         workflow.connect(
             [
-                (validation_and_dummies_wf, extract_roi, [('outputnode.pet_file', 'in_file')]),
+                (val_pet, extract_roi, [('out_file', 'in_file')]),
                 (extract_roi, outputnode, [('roi_file', 'petref')]),
             ]
         )  # fmt:skip
@@ -160,96 +142,27 @@ def init_validation_and_dummies_wf(
     pet_file=None,
     name='validation_and_dummies_wf',
 ):
-    """
-    Build a workflow that validates a PET image and detects non-steady-state volumes.
-
-    Workflow Graph
-        .. workflow::
-            :graph2use: orig
-            :simple_form: yes
-
-            from fmriprep.workflows.pet.reference import init_validation_and_dummies_wf
-            wf = init_validation_and_dummies_wf()
-
-    Parameters
-    ----------
-    pet_file : :obj:`str`
-        PET series NIfTI file
-    name : :obj:`str`
-        Name of workflow (default: ``validation_and_dummies_wf``)
-
-    Inputs
-    ------
-    pet_file : str
-        PET series NIfTI file
-    dummy_scans : int or None
-        Number of non-steady-state volumes specified by user at beginning of ``pet_file``
-
-    Outputs
-    -------
-    pet_file : str
-        Validated PET series NIfTI file
-    skip_vols : int
-        Number of non-steady-state volumes selected at beginning of ``pet_file``
-    algo_dummy_scans : int
-        Number of non-steady-state volumes agorithmically detected at
-        beginning of ``pet_file``
-
-    """
-    from niworkflows.interfaces.bold import NonsteadyStatesDetector
+    """Build a workflow that validates a PET image."""
 
     workflow = Workflow(name=name)
 
-    inputnode = pe.Node(
-        niu.IdentityInterface(fields=['pet_file', 'dummy_scans']),
-        name='inputnode',
-    )
+    inputnode = pe.Node(niu.IdentityInterface(fields=['pet_file']), name='inputnode')
     outputnode = pe.Node(
-        niu.IdentityInterface(
-            fields=[
-                'pet_file',
-                'skip_vols',
-                'algo_dummy_scans',
-                't_mask',
-                'validation_report',
-            ]
-        ),
+        niu.IdentityInterface(fields=['pet_file', 'validation_report']),
         name='outputnode',
     )
 
-    # Simplify manually setting input image
     if pet_file is not None:
         inputnode.inputs.pet_file = pet_file
 
-    val_pet = pe.Node(
-        ValidateImage(),
-        name='val_pet',
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
-
-    get_dummy = pe.Node(NonsteadyStatesDetector(), name='get_dummy')
-
-    calc_dummy_scans = pe.Node(
-        niu.Function(function=pass_dummy_scans, output_names=['skip_vols_num']),
-        name='calc_dummy_scans',
-        run_without_submitting=True,
-        mem_gb=DEFAULT_MEMORY_MIN_GB,
-    )
+    val_pet = pe.Node(ValidateImage(), name='val_pet', mem_gb=DEFAULT_MEMORY_MIN_GB)
 
     workflow.connect([
         (inputnode, val_pet, [('pet_file', 'in_file')]),
         (val_pet, outputnode, [
             ('out_file', 'pet_file'),
             ('out_report', 'validation_report'),
         ]),
-        (inputnode, get_dummy, [('pet_file', 'in_file')]),
-        (inputnode, calc_dummy_scans, [('dummy_scans', 'dummy_scans')]),
-        (get_dummy, calc_dummy_scans, [('n_dummy', 'algo_dummy_scans')]),
-        (get_dummy, outputnode, [
-            ('n_dummy', 'algo_dummy_scans'),
-            ('t_mask', 't_mask'),
-        ]),
-        (calc_dummy_scans, outputnode, [('skip_vols_num', 'skip_vols')]),
-    ])  # fmt:skip
+    ])
 
     return workflow