ENH: Overhaul fit workflow with upstream fmriprep changes

env.yml

@@ -29,8 +29,6 @@ dependencies:
 - ants=2.6
 # Workflow dependencies: Connectome Workbench
 - connectome-workbench-cli=2.0
-# Workflow dependencies: Convert3d
-- convert3d=1.4
 # Workflow dependencies: FSL (versions pinned in 6.0.7.17.20250415.fe1c582e)
 - fsl-bet2=2111.8
 - fsl-flirt=2111.4

nibabies/interfaces/resampling.py

@@ -2,12 +2,11 @@
 
 import asyncio
 import os
-from collections.abc import Callable
 from functools import partial
-from typing import TypeVar
 
 import nibabel as nb
 import nitransforms as nt
+import nitransforms.resampling
 import numpy as np
 from nipype.interfaces.base import (
     File,
@@ -22,23 +21,15 @@
 from sdcflows.transform import grid_bspline_weights
 from sdcflows.utils.tools import ensure_positive_cosines
 
-from nibabies.utils.transforms import load_transforms
-
-R = TypeVar('R')
-
-
-async def worker(job: Callable[[], R], semaphore: asyncio.Semaphore) -> R:
-    async with semaphore:
-        loop = asyncio.get_running_loop()
-        return await loop.run_in_executor(None, job)
+from ..utils.asynctools import worker
+from ..utils.transforms import load_transforms
 
 
 class ResampleSeriesInputSpec(TraitedSpec):
     in_file = File(exists=True, mandatory=True, desc='3D or 4D image file to resample')
     ref_file = File(exists=True, mandatory=True, desc='File to resample in_file to')
     transforms = InputMultiObject(
         File(exists=True),
-        mandatory=True,
         desc='Transform files, from in_file to ref_file (image mode)',
     )
     inverse = InputMultiObject(
@@ -100,7 +91,8 @@ def _run_interface(self, runtime):
 
         nvols = source.shape[3] if source.ndim > 3 else 1
 
-        transforms = load_transforms(self.inputs.transforms, self.inputs.inverse)
+        # No transforms appear Undefined, pass as empty list
+        transforms = load_transforms(self.inputs.transforms or [], self.inputs.inverse)
 
         pe_dir = self.inputs.pe_dir
         ro_time = self.inputs.ro_time
@@ -199,6 +191,13 @@ def _run_interface(self, runtime):
 class DistortionParametersInputSpec(TraitedSpec):
     in_file = File(exists=True, desc='EPI image corresponding to the metadata')
     metadata = traits.Dict(mandatory=True, desc='metadata corresponding to the inputs')
+    fallback = traits.Either(
+        None,
+        'estimated',
+        traits.Float,
+        usedefault=True,
+        desc='Fallback value for missing metadata',
+    )
 
 
 class DistortionParametersOutputSpec(TraitedSpec):
@@ -223,6 +222,8 @@ def _run_interface(self, runtime):
             self._results['readout_time'] = get_trt(
                 self.inputs.metadata,
                 self.inputs.in_file or None,
+                use_estimate=self.inputs.fallback == 'estimated',
+                fallback=self.inputs.fallback if isinstance(self.inputs.fallback, float) else None,
             )
             self._results['pe_direction'] = self.inputs.metadata['PhaseEncodingDirection']
         except (KeyError, ValueError):
@@ -686,9 +687,6 @@ def reconstruct_fieldmap(
             target.__class__(target.dataobj, projected_affine, target.header),
         )
     else:
-        # Below if statement was taken from fmriprep pull request #3439,
-        # along with the same explanation:
-        #
         # Hack. Sometimes the reference array is rotated relative to the fieldmap
         # and coefficient grids. As far as I know, coefficients are always RAS,
         # but good to check before doing this.
@@ -717,7 +715,7 @@ def reconstruct_fieldmap(
     )
 
     if not direct:
-        fmap_img = nt.apply(transforms, fmap_img, reference=target)
+        fmap_img = nt.resampling.apply(transforms, fmap_img, reference=target)
 
     fmap_img.header.set_intent('estimate', name='fieldmap Hz')
     fmap_img.header.set_data_dtype('float32')

nibabies/workflows/bold/base.py

@@ -734,8 +734,8 @@ def init_bold_wf(
         ]),
         (bold_fit_wf, bold_confounds_wf, [
             ('outputnode.bold_mask', 'inputnode.bold_mask'),
-            ('outputnode.movpar_file', 'inputnode.movpar_file'),
-            ('outputnode.rmsd_file', 'inputnode.rmsd_file'),
+            ('outputnode.hmc_boldref', 'inputnode.hmc_boldref'),
+            ('outputnode.motion_xfm', 'inputnode.motion_xfm'),
             ('outputnode.boldref2anat_xfm', 'inputnode.boldref2anat_xfm'),
             ('outputnode.dummy_scans', 'inputnode.skip_vols'),
         ]),

nibabies/workflows/bold/confounds.py

@@ -31,6 +31,11 @@
 from nipype.algorithms import confounds as nac
 from nipype.interfaces import utility as niu
 from nipype.pipeline import engine as pe
+from niworkflows.interfaces.confounds import (
+    FramewiseDisplacement,
+    FSLMotionParams,
+    FSLRMSDeviation,
+)
 
 from nibabies.config import DEFAULT_DISMISS_ENTITIES, DEFAULT_MEMORY_MIN_GB
 from nibabies.interfaces import DerivativesDataSink
@@ -118,10 +123,10 @@ def init_bold_confs_wf(
         when available.
     bold_mask
         BOLD series mask
-    movpar_file
-        SPM-formatted motion parameters file
-    rmsd_file
-        Root mean squared deviation as measured by ``fsl_motion_outliers`` [Jenkinson2002]_.
+    motion_xfm
+        ITK-formatted head motion transforms
+    hmc_boldref
+        BOLD volume after HMC
     skip_vols
         number of non steady state volumes
     anat_mask
@@ -219,8 +224,8 @@ def init_bold_confs_wf(
             fields=[
                 'bold',
                 'bold_mask',
-                'movpar_file',
-                'rmsd_file',
+                'motion_xfm',
+                'hmc_boldref',
                 'skip_vols',
                 'anat_mask',
                 'anat_tpms',
@@ -260,8 +265,12 @@ def init_bold_confs_wf(
         mem_gb=mem_gb,
     )
 
+    # Motion parameters
+    motion_params = pe.Node(FSLMotionParams(), name='motion_params')
+
     # Frame displacement
-    fdisp = pe.Node(nac.FramewiseDisplacement(parameter_source='SPM'), name='fdisp', mem_gb=mem_gb)
+    fdisp = pe.Node(FramewiseDisplacement(), name='fdisp')
+    rmsd = pe.Node(FSLRMSDeviation(), name='rmsd')
 
     # Generate aCompCor probseg maps
     acc_masks = pe.Node(aCompCorMasks(is_aseg=freesurfer), name='acc_masks')
@@ -365,18 +374,6 @@ def init_bold_confs_wf(
         mem_gb=0.01,
         run_without_submitting=True,
     )
-    add_motion_headers = pe.Node(
-        AddTSVHeader(columns=['trans_x', 'trans_y', 'trans_z', 'rot_x', 'rot_y', 'rot_z']),
-        name='add_motion_headers',
-        mem_gb=0.01,
-        run_without_submitting=True,
-    )
-    add_rmsd_header = pe.Node(
-        AddTSVHeader(columns=['rmsd']),
-        name='add_rmsd_header',
-        mem_gb=0.01,
-        run_without_submitting=True,
-    )
     concat = pe.Node(GatherConfounds(), name='concat', mem_gb=0.01, run_without_submitting=True)
 
     # CompCor metadata
@@ -529,7 +526,11 @@ def _select_cols(table):
         # connect inputnode to each non-anatomical confound node
         (inputnode, dvars, [('bold', 'in_file'),
                             ('bold_mask', 'in_mask')]),
-        (inputnode, fdisp, [('movpar_file', 'in_file')]),
+        (inputnode, motion_params, [('motion_xfm', 'xfm_file'),
+                                    ('hmc_boldref', 'boldref_file')]),
+        (inputnode, rmsd, [('motion_xfm', 'xfm_file'),
+                           ('hmc_boldref', 'boldref_file')]),
+        (motion_params, fdisp, [('out_file', 'in_file')]),
         # Brain mask
         (inputnode, anat_mask_tfm, [('anat_mask', 'input_image'),
                                    ('bold_mask', 'reference_image'),
@@ -572,8 +573,6 @@ def _select_cols(table):
         (merge_rois, signals, [('out', 'label_files')]),
 
         # Collate computed confounds together
-        (inputnode, add_motion_headers, [('movpar_file', 'in_file')]),
-        (inputnode, add_rmsd_header, [('rmsd_file', 'in_file')]),
         (dvars, add_dvars_header, [('out_nstd', 'in_file')]),
         (dvars, add_std_dvars_header, [('out_std', 'in_file')]),
         (signals, concat, [('out_file', 'signals')]),
@@ -582,8 +581,8 @@ def _select_cols(table):
                             ('pre_filter_file', 'cos_basis')]),
         (rename_acompcor, concat, [('components_file', 'acompcor')]),
         (crowncompcor, concat, [('components_file', 'crowncompcor')]),
-        (add_motion_headers, concat, [('out_file', 'motion')]),
-        (add_rmsd_header, concat, [('out_file', 'rmsd')]),
+        (motion_params, concat, [('out_file', 'motion')]),
+        (rmsd, concat, [('out_file', 'rmsd')]),
         (add_dvars_header, concat, [('out_file', 'dvars')]),
         (add_std_dvars_header, concat, [('out_file', 'std_dvars')]),