ENH: Add MCRIBS interface

Author: mgxd

nibabies/interfaces/mcribs.py

@@ -0,0 +1,187 @@
+import os
+import shutil
+from pathlib import Path
+
+from nipype.interfaces.base import (
+    CommandLine,
+    CommandLineInputSpec,
+    Directory,
+    File,
+    TraitedSpec,
+    traits,
+)
+
+
+class MCRIBReconAllInputSpec(CommandLineInputSpec):
+    # Input structure massaging
+    subjects_dir = Directory(
+        exists=True,
+        hash_files=False,
+        desc='path to subjects directory',
+        required=True,
+    )
+    subject_id = traits.Str(
+        # required=True,
+        argstr='%s',
+        position=-1,
+        desc='subject name',
+    )
+    t1w_file = File(
+        exists=True,
+        copyfile=True,
+        desc='T1w to be used for deformable (must be registered to T2w image)',
+    )
+    t2w_file = File(
+        exists=True,
+        required=True,
+        copyfile=True,
+        desc='T2w (Isotropic + N4 corrected)',
+    )
+    segmentation_file = File(
+        desc='Segmentation file (skips tissue segmentation)',
+    )
+
+    # MCRIBS options
+    conform = traits.Bool(
+        argstr='--conform',
+        desc='Reorients to radiological, axial slice orientation. Resamples to isotropic voxels',
+    )
+    tissueseg = traits.Bool(
+        argstr='--tissueseg',
+        desc='Perform tissue type segmentation',
+    )
+    surfrecon = traits.Bool(
+        True,
+        usedefault=True,
+        argstr='--surfrecon',
+        desc='Reconstruct surfaces',
+    )
+    surfrecon_method = traits.Enum(
+        'Deformable',
+        argstr='--surfreconmethod %s',
+        usedefault=True,
+        desc='Surface reconstruction method',
+    )
+    join_thresh = traits.Float(
+        1.0,
+        argstr='--deformablejointhresh %f',
+        usedefault=True,
+        desc='Join threshold parameter for Deformable',
+    )
+    fast_collision = traits.Bool(
+        True,
+        argstr='--deformablefastcollision',
+        usedefault=True,
+        desc='Use Deformable fast collision test',
+    )
+    autorecon_after_surf = traits.Bool(
+        True,
+        argstr='--autoreconaftersurf',
+        usedefault=True,
+        desc='Do all steps after surface reconstruction',
+    )
+    segstats = traits.Bool(
+        True,
+        argstr='--segstats',
+        usedefault=True,
+        desc='Compute statistics on segmented volumes',
+    )
+    nthreads = traits.Int(
+        argstr='-nthreads %d',
+        desc='Number of threads for multithreading applications',
+    )
+
+
+class MCRIBReconAllOutputSpec(TraitedSpec):
+    mcribs_dir = Directory(desc='MCRIBS output directory')
+
+
+class MCRIBReconAll(CommandLine):
+    _cmd = 'MCRIBReconAll'
+    input_spec = MCRIBReconAllInputSpec
+    output_spec = MCRIBReconAllOutputSpec
+
+    def _setup_directory_structure(self, mcribs_dir: Path) -> None:
+        '''
+        Create the required structure for skipping steps.
+
+        The directory tree
+        ------------------
+
+        <subject_id>/
+        ├── RawT2
+        │   └── <subject_id>.nii.gz
+        ├── SurfReconDeformable
+        │   └── <subject_id>
+        │       └── temp
+        │           └── t2w-image.nii.gz
+        ├── TissueSeg
+        │   ├── <subject_id>_all_labels.nii.gz
+        │   └── <subject_id>_all_labels_manedit.nii.gz
+        └── TissueSegDrawEM
+            └── <subject_id>
+                └── N4
+                    └── <subject_id>.nii.gz
+        '''
+        sid = self.inputs.subject_id
+        mkdir_kw = {'parents': True, 'exist_ok': True}
+        root = mcribs_dir / sid
+        root.mkdir(**mkdir_kw)
+
+        # T2w operations
+        t2w = root / 'RawT2' / f'{sid}.nii.gz'
+        t2w.parent.mkdir(**mkdir_kw)
+        if not t2w.exists():
+            shutil.copy(self.inputs.t2w_file, str(t2w))
+
+        if not self.inputs.conform:
+            t2wiso = root / 'RawT2RadiologicalIsotropic' / f'{sid}.nii.gz'
+            t2wiso.parent.mkdir(**mkdir_kw)
+            if not t2wiso.exists():
+                t2wiso.symlink_to(f'../../RawT2/{sid}.nii.gz')
+
+            n4 = root / sid / 'N4' / f'{sid}.nii.gz'
+            n4.parent.mkdir(**mkdir_kw)
+            if not n4.exists():
+                n4.symlink_to(f'../../../RawT2/{sid}.nii.gz')
+
+        # Segmentation
+        if self.inputs.segmentation_file:
+            # TissueSeg directive disabled
+            tisseg = root / 'TissueSeg' / f'{sid}_all_labels.nii.gz'
+            tisseg.parent.mkdir(**mkdir_kw)
+            if not tisseg.exists():
+                shutil.copy(self.inputs.segmentation, str(tisseg))
+            manedit = tisseg.parent / f'{sid}_all_labels_manedit.nii.gz'
+            if not manedit.exists():
+                manedit.symlink_to(tisseg.name)
+
+            if self.inputs.surfrecon:
+                surfrec = root / 'SurfReconDeformable' / sid / 'temp' / 't2w-image.nii.gz'
+                surfrec.parent.mkdir(**mkdir_kw)
+                if not surfrec.exists():
+                    surfrec.symlink_to(f'../../../../RawT2/{sid}.nii.gz')
+
+        # TODO: T1w -> <subject_id>/RawT1RadiologicalIsotropic/<subjectid>.nii.gz
+        return
+
+    def _run_interface(self, runtime):
+        # if users wish to preserve their runs
+        mcribs_dir = os.getenv('MCRIBS_SUBJECTS')
+        if mcribs_dir is None or not Path(mcribs_dir).exists():
+            mcribs_dir = runtime.cwd / 'mcribs'
+        self._mcribs_dir = mcribs_dir
+        self._setup_directory_structure(mcribs_dir)
+        # runs in CWD
+        os.chdir(mcribs_dir / self.inputs.subject_id)
+        return super()._run_interface(runtime)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['mcribs_dir'] = self._mcribs_dir
+
+        # TODO: Copy freesurfer directory into FS subjects dir
+        # fs_outputs = self._mcribs_dir / self.inputs.subject_id / 'freesurfer'
+        # if fs_outputs.exists():
+        #     pass
+        return outputs