Merge pull request #125 from slimnsour/enh/bbreg

ENH: Port bbregister T1-to-dwi registration from fmriprep

Author: oesteban

.maint/developers.json

@@ -22,6 +22,11 @@
     "name": "Lerma-Usabiaga, Garikoitz",
     "orcid": "0000-0001-9800-4816"
   },
+  {
+     "affiliation": "The Centre for Addiction and Mental Health",
+     "name": "Mansour, Salim",
+     "orcid": "0000-0002-1092-1650"
+  },
   {
     "affiliation": "Department of Psychology, University of Texas at Austin, TX, USA",
     "name": "Pisner, Derek",

dmriprep/cli/parser.py

@@ -191,7 +191,7 @@ def _bids_filter(value):
         action="store",
         nargs="+",
         default=[],
-        choices=["fieldmaps", "slicetiming", "sbref"],
+        choices=["fieldmaps", "sbref"],
         help="ignore selected aspects of the input dataset to disable corresponding "
         "parts of the workflow (a space delimited list)",
     )
@@ -219,6 +219,14 @@ def _bids_filter(value):
 https://www.nipreps.org/dmriprep/en/%s/spaces.html"""
         % (currentv.base_version if is_release else "latest"),
     )
+    g_conf.add_argument(
+        "--dwi2t1w-init",
+        action="store",
+        default="register",
+        choices=["register", "header"],
+        help='Either "register" (the default) to initialize volumes at center or "header"'
+        " to use the header information when coregistering DWI to T1w images.",
+    )
 
     #  ANTs options
     g_ants = parser.add_argument_group("Specific options for ANTs registrations")

dmriprep/config/__init__.py

@@ -425,6 +425,9 @@ class workflow(_Config):
 
     anat_only = False
     """Execute the anatomical preprocessing only."""
+    dwi2t1w_init = "register"
+    """Whether to use standard coregistration ('register') or to initialize coregistration from the
+    DWI header ('header')."""
     fmap_bspline = None
     """Regularize fieldmaps with a field of B-Spline basis."""
     fmap_demean = None

dmriprep/config/reports-spec.yml

@@ -49,6 +49,23 @@ sections:
       all b=0 found in the dataset, after accounting for signal drift.
       The red contour shows the brain mask calculated using this reference b=0.
     subtitle: Reference b=0 and brain mask
+  - bids: {datatype: figures, desc: coreg, suffix: dwi}
+    caption: Diffusion-weighted data and anatomical data (EPI-space and T1w-space)
+      were aligned with <code>mri_coreg</code> (FreeSurfer).
+      WARNING - <code>bbregister</code> refinement rejected.
+    description: Note that nearest-neighbor interpolation is used in this reportlet
+      in order to highlight potential slice Inhomogeneities and other artifacts, whereas
+      the final images are resampled using cubic B-Spline interpolation.
+    static: false
+    subtitle: Alignment of functional and anatomical MRI data (volume based)
+  - bids: {datatype: figures, desc: bbregister, suffix: dwi}
+    caption: Diffusion-weighted data and anatomical data (EPI-space and T1w-space)
+      were aligned with <code>bbregister</code> (FreeSurfer).
+    description: Note that nearest-neighbor interpolation is used in this reportlet
+      in order to highlight potential slice Inhomogeneities and other artifacts, whereas
+      the final images are resampled using cubic B-Spline interpolation.
+    static: false
+    subtitle: Alignment of functional and anatomical MRI data (surface driven)
 - name: About
   reportlets:
   - bids: {datatype: figures, desc: about, suffix: T1w}

dmriprep/workflows/base.py

@@ -12,6 +12,7 @@
 from niworkflows.utils.misc import fix_multi_T1w_source_name
 from niworkflows.utils.spaces import Reference
 from smriprep.workflows.anatomical import init_anat_preproc_wf
+from fmriprep.workflows.bold.registration import init_bbreg_wf
 
 from ..interfaces import DerivativesDataSink, BIDSDataGrabber
 from ..interfaces.reports import SubjectSummary, AboutSummary
@@ -287,7 +288,7 @@ def init_single_subject_wf(subject_id):
         return workflow
 
     # Append the dMRI section to the existing anatomical excerpt
-    # That way we do not need to stream down the number of bold datasets
+    # That way we do not need to stream down the number of DWI datasets
     anat_preproc_wf.__postdesc__ = (
         (anat_preproc_wf.__postdesc__ or "")
         + f"""
@@ -354,6 +355,53 @@ def init_single_subject_wf(subject_id):
     ])
     # fmt:on
 
+    if config.workflow.run_reconall:
+        from niworkflows.interfaces.nibabel import ApplyMask
+
+        # Mask the T1w
+        t1w_brain = pe.Node(ApplyMask(), name="t1w_brain")
+
+        bbr_wf = init_bbreg_wf(
+            bold2t1w_dof=6,
+            bold2t1w_init=config.workflow.dwi2t1w_init,
+            omp_nthreads=config.nipype.omp_nthreads,
+            use_bbr=True,
+        )
+
+        ds_report_reg = pe.Node(
+            DerivativesDataSink(base_directory=str(output_dir), datatype="figures",),
+            name="ds_report_reg",
+            run_without_submitting=True,
+        )
+
+        def _bold_reg_suffix(fallback):
+            return "coreg" if fallback else "bbregister"
+
+        # fmt:off
+        workflow.connect([
+            # T1w Mask
+            (anat_preproc_wf, t1w_brain, [
+                ("outputnode.t1w_preproc", "in_file"),
+                ("outputnode.t1w_mask", "in_mask"),
+            ]),
+            # BBRegister
+            (early_b0ref_wf, bbr_wf, [
+                ("outputnode.dwi_reference", "inputnode.in_file")
+            ]),
+            (t1w_brain, bbr_wf, [("out_file", "inputnode.t1w_brain")]),
+            (anat_preproc_wf, bbr_wf, [("outputnode.t1w_dseg", "inputnode.t1w_dseg")]),
+            (fsinputnode, bbr_wf, [("subjects_dir", "inputnode.subjects_dir")]),
+            (bids_info, bbr_wf, [(("subject", _prefix), "inputnode.subject_id")]),
+            (anat_preproc_wf, bbr_wf, [
+                ("outputnode.fsnative2t1w_xfm", "inputnode.fsnative2t1w_xfm")
+            ]),
+            (split_info, ds_report_reg, [("dwi_file", "source_file")]),
+            (bbr_wf, ds_report_reg, [
+                ('outputnode.out_report', 'in_file'),
+                (('outputnode.fallback', _bold_reg_suffix), 'desc')]),
+        ])
+        # fmt:on
+
     fmap_estimation_wf = init_fmap_estimation_wf(
         subject_data["dwi"], debug=config.execution.debug
     )

docs/requirements.txt

@@ -1,5 +1,6 @@
 git+https://github.com/AleksandarPetrov/napoleon.git@0dc3f28a309ad602be5f44a9049785a1026451b3#egg=sphinxcontrib-napoleon
 git+https://github.com/rwblair/sphinxcontrib-versioning.git@39b40b0b84bf872fc398feff05344051bbce0f63#egg=sphinxcontrib-versioning
+fmriprep
 nbsphinx
 nipype ~= 1.4
 git+https://github.com/nipreps/niworkflows.git@master#egg=niworkflows

setup.cfg

@@ -33,6 +33,7 @@ install_requires =
     smriprep ~= 0.7.0 
     templateflow ~= 0.6
     toml
+    fmriprep ~= 20.2
 setup_requires =
     setuptools >= 40.8.0
 test_requires =