FEAT: Option to normalize CSF prior to template registration

nibabies/cli/parser.py

@@ -753,6 +753,11 @@ def _str_none(val):
         default=16,
         help='Frame to start head motion estimation on BOLD.',
     )
+    g_baby.add_argument(
+        '--norm-csf',
+        action='store_true',
+        help='Replace low intensity voxels in CSF mask with average',
+    )
     return parser
 
 

nibabies/config.py

@@ -578,6 +578,8 @@ class workflow(_Config):
     """Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
     medial_surface_nan = None
     """Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
+    norm_csf = False
+    """Replace low intensity voxels in CSF mask with average."""
     project_goodvoxels = False
     """Exclude voxels with locally high coefficient of variation from sampling."""
     regressors_all_comps = None

nibabies/workflows/anatomical/fit.py

@@ -36,7 +36,7 @@
 from nibabies import config
 from nibabies.workflows.anatomical.brain_extraction import init_infant_brain_extraction_wf
 from nibabies.workflows.anatomical.outputs import init_anat_reports_wf
-from nibabies.workflows.anatomical.preproc import init_anat_preproc_wf
+from nibabies.workflows.anatomical.preproc import init_anat_preproc_wf, init_csf_norm_wf
 from nibabies.workflows.anatomical.registration import init_coregistration_wf
 from nibabies.workflows.anatomical.segmentation import init_segmentation_wf
 from nibabies.workflows.anatomical.surfaces import init_mcribs_dhcp_wf
@@ -184,6 +184,14 @@
         name='anat_buffer',
     )
 
+    # Additional buffer if CSF normalization is used
+    anat_preproc_buffer = pe.Node(
+        niu.IdentityInterface(fields=['anat_preproc']),
+        name='anat_preproc_buffer',
+    )
+    if not config.workflow.norm_csf:
+        workflow.connect(anat_buffer, 'anat_preproc', anat_preproc_buffer, 'anat_preproc')
+
     if reference_anat == 'T1w':
         LOGGER.info('ANAT: Using T1w as the reference anatomical')
         workflow.connect([
@@ -248,7 +256,7 @@
     msm_buffer = pe.Node(niu.IdentityInterface(fields=['sphere_reg_msm']), name='msm_buffer')
 
     workflow.connect([
-        (anat_buffer, outputnode, [
+        (anat_preproc_buffer, outputnode, [
             ('anat_preproc', 'anat_preproc'),
         ]),
         (refined_buffer, outputnode, [
@@ -637,24 +645,6 @@
                     (binarize_t2w, t2w_buffer, [('out_file', 't2w_mask')]),
                 ])  # fmt:skip
         else:
-            # Check whether we can convert a previously computed T2w mask
-            # or need to run the atlas based brain extraction
-
-            # if t1w_mask:
-            #     LOGGER.info('ANAT T1w mask will be transformed into T2w space')
-            #     transform_t1w_mask = pe.Node(
-            #         ApplyTransforms(interpolation='MultiLabel'),
-            #         name='transform_t1w_mask',
-            #     )
-
-            #     workflow.connect([
-            #         (t1w_buffer, transform_t1w_mask, [('t1w_mask', 'input_image')]),
-            #         (coreg_buffer, transform_t1w_mask, [('t1w2t2w_xfm', 'transforms')]),
-            #         (transform_t1w_mask, apply_t2w_mask, [('output_image', 'in_mask')]),
-            #         (t2w_buffer, apply_t1w_mask, [('t2w_preproc', 'in_file')]),
-            #         # TODO: Unsure about this connection^
-            #     ])  # fmt:skip
-            # else:
             LOGGER.info('ANAT Atlas-based brain mask will be calculated on the T2w')
             brain_extraction_wf = init_infant_brain_extraction_wf(
                 omp_nthreads=omp_nthreads,
@@ -898,6 +888,15 @@
     anat2std_buffer.inputs.in1 = [xfm['forward'] for xfm in found_xfms.values()]
     std2anat_buffer.inputs.in1 = [xfm['reverse'] for xfm in found_xfms.values()]
 
+    if config.workflow.norm_csf:
+        csf_norm_wf = init_csf_norm_wf()
+
+        workflow.connect([
+            (anat_buffer, csf_norm_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
+            (seg_buffer, csf_norm_wf, [('anat_tpms', 'inputnode.anat_tpms')]),
+            (csf_norm_wf, anat_preproc_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
+        ])  # fmt:skip
+
     if templates:
         LOGGER.info(f'ANAT Stage 5: Preparing normalization workflow for {templates}')
         register_template_wf = init_register_template_wf(
@@ -913,7 +912,9 @@
 
         workflow.connect([
             (inputnode, register_template_wf, [('roi', 'inputnode.lesion_mask')]),
-            (anat_buffer, register_template_wf, [('anat_preproc', 'inputnode.moving_image')]),
+            (anat_preproc_buffer, register_template_wf, [
+                ('anat_preproc', 'inputnode.moving_image'),
+            ]),
             (refined_buffer, register_template_wf, [('anat_mask', 'inputnode.moving_mask')]),
             (sourcefile_buffer, ds_template_registration_wf, [
                 ('anat_source_files', 'inputnode.source_files')
@@ -1106,7 +1107,7 @@
             (seg_buffer, refinement_wf, [
                 ('ants_segs', 'inputnode.ants_segs'),  # TODO: Verify this is the same as dseg
             ]),
-            (anat_buffer, applyrefined, [('anat_preproc', 'in_file')]),
+            (anat_preproc_buffer, applyrefined, [('anat_preproc', 'in_file')]),
             (refinement_wf, applyrefined, [('outputnode.out_brainmask', 'in_mask')]),
             (refinement_wf, refined_buffer, [('outputnode.out_brainmask', 'anat_mask')]),
             (applyrefined, refined_buffer, [('out_file', 'anat_brain')]),
@@ -1384,6 +1385,14 @@
         name='anat_buffer',
     )
 
+    # Additional buffer if CSF normalization is used
+    anat_preproc_buffer = pe.Node(
+        niu.IdentityInterface(fields=['anat_preproc']),
+        name='anat_preproc_buffer',
+    )
+    if not config.workflow.norm_csf:
+        workflow.connect(anat_buffer, 'anat_preproc', anat_preproc_buffer, 'anat_preproc')
+
     aseg_buffer = pe.Node(
         niu.IdentityInterface(fields=['anat_aseg']),
         name='aseg_buffer',
@@ -1423,7 +1432,7 @@
     msm_buffer = pe.Node(niu.IdentityInterface(fields=['sphere_reg_msm']), name='msm_buffer')
 
     workflow.connect([
-        (anat_buffer, outputnode, [
+        (anat_preproc_buffer, outputnode, [
             ('anat_preproc', 'anat_preproc'),
         ]),
         (refined_buffer, outputnode, [
@@ -1724,6 +1733,15 @@
     anat2std_buffer.inputs.in1 = [xfm['forward'] for xfm in found_xfms.values()]
     std2anat_buffer.inputs.in1 = [xfm['reverse'] for xfm in found_xfms.values()]
 
+    if config.workflow.norm_csf:
+        csf_norm_wf = init_csf_norm_wf()
+
+        workflow.connect([
+            (anat_buffer, csf_norm_wf, [('anat_preproc', 'inputnode.anat_preproc')]),
+            (seg_buffer, csf_norm_wf, [('anat_tpms', 'inputnode.anat_tpms')]),
+            (csf_norm_wf, anat_preproc_buffer, [('outputnode.anat_preproc', 'anat_preproc')]),
+        ])  # fmt:skip
+
     if templates:
         LOGGER.info(f'ANAT Stage 4: Preparing normalization workflow for {templates}')
         register_template_wf = init_register_template_wf(
@@ -1739,7 +1757,9 @@
 
         workflow.connect([
             (inputnode, register_template_wf, [('roi', 'inputnode.lesion_mask')]),
-            (anat_buffer, register_template_wf, [('anat_preproc', 'inputnode.moving_image')]),
+            (anat_preproc_buffer, register_template_wf, [
+                ('anat_preproc', 'inputnode.moving_image'),
+            ]),
             (refined_buffer, register_template_wf, [('anat_mask', 'inputnode.moving_mask')]),
             (sourcefile_buffer, ds_template_registration_wf, [
                 ('anat_source_files', 'inputnode.source_files')
@@ -1921,7 +1941,7 @@
             (seg_buffer, refinement_wf, [
                 ('ants_segs', 'inputnode.ants_segs'),
             ]),
-            (anat_buffer, applyrefined, [('anat_preproc', 'in_file')]),
+            (anat_preproc_buffer, applyrefined, [('anat_preproc', 'in_file')]),
             (refinement_wf, applyrefined, [('outputnode.out_brainmask', 'in_mask')]),
             (refinement_wf, refined_buffer, [('outputnode.out_brainmask', 'anat_mask')]),
             (applyrefined, refined_buffer, [('out_file', 'anat_brain')]),

nibabies/workflows/anatomical/preproc.py

@@ -66,3 +66,56 @@ def init_anat_preproc_wf(
         (final_clip, outputnode, [('out_file', 'anat_preproc')]),
     ])  # fmt:skip
     return wf
+
+
+def init_csf_norm_wf(name: str = 'csf_norm_wf') -> LiterateWorkflow:
+    """Replace low intensity voxels within the CSF mask with the median value."""
+
+    workflow = LiterateWorkflow(name=name)
+    workflow.__desc__ = (
+        'The CSF mask was used to normalize the anatomical template by the median of voxels '
+        'within the mask.'
+    )
+    inputnode = pe.Node(
+        niu.IdentityInterface(fields=['anat_preproc', 'anat_tpms']),
+        name='inputnode',
+    )
+    outputnode = pe.Node(niu.IdentityInterface(fields=['anat_preproc']), name='outputnode')
+
+    # select CSF from BIDS-ordered list (GM, WM, CSF)
+    select_csf = pe.Node(niu.Select(index=2), name='select_csf')
+    norm_csf = pe.Node(niu.Function(function=_normalize_roi), name='norm_csf')
+
+    workflow.connect([
+        (inputnode, select_csf, [('anat_tpms', 'inlist')]),
+        (select_csf, norm_csf, [('out', 'mask_file')]),
+        (inputnode, norm_csf, [('anat_preproc', 'in_file')]),
+        (norm_csf, outputnode, [('out', 'anat_preproc')]),
+    ])  # fmt:skip
+
+    return workflow
+
+
+def _normalize_roi(in_file, mask_file, threshold=0.2, out_file=None):
+    """Normalize low intensity voxels that fall within a given mask."""
+    import nibabel as nb
+    import numpy as np
+
+    img = nb.load(in_file)
+    img_data = np.asanyarray(img.dataobj)
+    mask_img = nb.load(mask_file)
+    # binary mask
+    bin_mask = np.asanyarray(mask_img.dataobj) > threshold
+    mask_data = bin_mask * img_data
+    masked_data = mask_data[mask_data > 0]
+
+    median = np.median(masked_data).astype(masked_data.dtype)
+    normed_data = np.maximum(img_data, bin_mask * median)
+
+    oimg = img.__class__(normed_data, img.affine, img.header)
+    if not out_file:
+        from nipype.utils.filemanip import fname_presuffix
+
+        out_file = fname_presuffix(in_file, suffix='normed')
+    oimg.to_filename(out_file)
+    return out_file

nibabies/workflows/anatomical/tests/test_preproc.py

@@ -0,0 +1,55 @@
+import typing as ty
+from pathlib import Path
+
+import nibabel as nb
+import numpy as np
+import pytest
+
+from nibabies.workflows.anatomical.preproc import _normalize_roi, init_csf_norm_wf
+
+EXPECTED_CSF_NORM = np.array([[[10, 73], [73, 29]], [[77, 80], [6, 16]]], dtype='uint8')
+
+
+@pytest.fixture
+def csf_norm_data(tmp_path) -> ty.Generator[tuple[Path, list[Path]], None, None]:
+    np.random.seed(10)
+
+    in_file = tmp_path / 'input.nii.gz'
+    data = np.random.randint(1, 101, size=(2, 2, 2), dtype='uint8')
+    img = nb.Nifti1Image(data, np.eye(4))
+    img.to_filename(in_file)
+
+    masks = []
+    for tpm in ('gm', 'wm', 'csf'):
+        name = tmp_path / f'{tpm}.nii.gz'
+        binmask = data > np.random.randint(10, 90)
+        masked = (binmask * 1).astype('uint8')
+        mask = nb.Nifti1Image(masked, img.affine)
+        mask.to_filename(name)
+        masks.append(name)
+
+    yield in_file, masks
+
+    in_file.unlink()
+    for m in masks:
+        m.unlink()
+
+
+def test_csf_norm_wf(tmp_path, csf_norm_data):
+    anat, tpms = csf_norm_data
+    wf = init_csf_norm_wf()
+    wf.base_dir = tmp_path
+
+    wf.inputs.inputnode.anat_preproc = anat
+    wf.inputs.inputnode.anat_tpms = tpms
+
+    # verify workflow runs
+    wf.run()
+
+    # verify function works as expected
+    outfile = _normalize_roi(anat, tpms[2])
+    assert np.array_equal(
+        np.asanyarray(nb.load(outfile).dataobj),
+        EXPECTED_CSF_NORM,
+    )
+    Path(outfile).unlink()

pyproject.toml

@@ -34,7 +34,7 @@ dependencies = [
     "requests",
     "sdcflows >= 2.10.0",
 #    "smriprep >= 0.16.1",
-    "smriprep @ git+https://github.com/nipreps/smriprep.git@master",
+    "smriprep @ git+https://github.com/nipreps/smriprep.git@dev-nibabies",
     "tedana >= 23.0.2",
     "templateflow >= 24.2.0",
     "toml",