Merge pull request #415 from mgxd/enh/mni-reg

ENH: Add flag for multi-step registration to adult templates

nibabies/cli/parser.py

@@ -758,6 +758,12 @@ def _str_none(val):
         action='store_true',
         help='Replace low intensity voxels in CSF mask with average',
     )
+    g_baby.add_argument(
+        '--multi-step-reg',
+        action='store_true',
+        help='For certain adult templates (MNI152NLin6Asym), perform two step '
+        'registrations (native -> MNIInfant -> template) and concatenate into a single xfm',
+    )
     return parser
 
 

nibabies/config.py

@@ -578,6 +578,9 @@ 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."""
+    multi_step_reg = False
+    """Perform multiple registrations (native -> MNIInfant -> template) and concatenate into a
+    single transform"""
     norm_csf = False
     """Replace low intensity voxels in CSF mask with average."""
     project_goodvoxels = False

nibabies/data/xfm_manifest.json

@@ -0,0 +1,90 @@
+{
+    "from-MNI152NLin6Asym_to-MNIInfant+10_xfm.h5": {
+        "url": "https://osf.io/download/jf6vz/",
+        "hash": "md5:df6d40e5bbdca85f083866ad26507796"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+11_xfm.h5": {
+        "url": "https://osf.io/download/zmjyn/",
+        "hash": "md5:ff8435f06c0a44be88e050492b90ffea"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+1_xfm.h5": {
+        "url": "https://osf.io/download/kx7ny/",
+        "hash": "md5:c27d35dff75d59d605c8d786c985594e"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+2_xfm.h5": {
+        "url": "https://osf.io/download/6758aa0c67a7782b00f73c77/",
+        "hash": "md5:81fabdc70c200bf099893bd1377ef0f7"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+3_xfm.h5": {
+        "url": "https://osf.io/download/6758aa1c76bfbc22cbf73b0a/",
+        "hash": "md5:c8f5b79b95f9aa65add5524e88601cc6"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+4_xfm.h5": {
+        "url": "https://osf.io/download/6758aa1bb96fd819c41e25a4/",
+        "hash": "md5:1e4b927115a76b031c46e6180fc76a30"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+5_xfm.h5": {
+        "url": "https://osf.io/download/6758aa146e0cd8ca5f563b2b/",
+        "hash": "md5:25bfd0837a88db267762974c0a530535"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+6_xfm.h5": {
+        "url": "https://osf.io/download/6758ab50b95a2e75b11e23f0/",
+        "hash": "md5:7ed4732832ed6dd45dd2259d8b4454e7"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+7_xfm.h5": {
+        "url": "https://osf.io/download/6758ab5667a7782b00f73cfa/",
+        "hash": "md5:a1244c38b7b4825abefc5834d0398b08"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+8_xfm.h5": {
+        "url": "https://osf.io/download/rq2an/",
+        "hash": "md5:50d11fdac22c6589af8a7f61e4b3e41a"
+    },
+    "from-MNI152NLin6Asym_to-MNIInfant+9_xfm.h5": {
+        "url": "https://osf.io/download/6758ab67eacdd8b34803d991/",
+        "hash": "md5:3184d91f8b3a386ca3ec913c365651d8"
+    },
+    "from-MNIInfant+10_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/4xh9q/",
+        "hash": "md5:a1f3dd3c0ac8b05efbaf893cca6f9641"
+    },
+    "from-MNIInfant+11_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a5026e0cd8ca5f56380d/",
+        "hash": "md5:0d1aadef884574e54065d4e2cdb8e398"
+    },
+    "from-MNIInfant+1_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/7ge2b/",
+        "hash": "md5:d5e4272140c6f582f64b7f39b31ca837"
+    },
+    "from-MNIInfant+2_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a3c1a678894ad71e2422/",
+        "hash": "md5:b03651dae4d378410c44f1c6c63dbea0"
+    },
+    "from-MNIInfant+3_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a3c3bc61ce5912662055/",
+        "hash": "md5:7cc099e26647e670c8e75ead2cfe39a6"
+    },
+    "from-MNIInfant+4_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a3bc040c053b58f73b47/",
+        "hash": "md5:e92e9150f2ad4d2730f005aa9750438d"
+    },
+    "from-MNIInfant+5_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a3bdea7294dbdd66161a/",
+        "hash": "md5:9cf6cf3fb500c229da15490c9080201a"
+    },
+    "from-MNIInfant+6_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a3bf040c053b58f73b4b/",
+        "hash": "md5:2212fdb57b85e8a0f7fa9feea5b0dd1b"
+    },
+    "from-MNIInfant+7_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a4f78af26d0a97661ca9/",
+        "hash": "md5:6913f8191201350311ff61525fae8a21"
+    },
+    "from-MNIInfant+8_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a500f82c189df71e256f/",
+        "hash": "md5:809455af8416cd61c1693b5c7eafbd13"
+    },
+    "from-MNIInfant+9_to-MNI152NLin6Asym_xfm.h5": {
+        "url": "https://osf.io/download/6758a4ff040c053b58f73bd1/",
+        "hash": "md5:49317cbb038c399d4df7428f07d36983"
+    }
+}

nibabies/interfaces/conftest.py

@@ -33,6 +33,8 @@ def _chdir(path):
     'sub-01_run-01_echo-1_bold.nii.gz',
     'sub-01_run-01_echo-2_bold.nii.gz',
     'sub-01_run-01_echo-3_bold.nii.gz',
+    'xfm0.h5',
+    'xfm1.h5',
 )
 
 

nibabies/interfaces/patches.py

@@ -1,5 +1,10 @@
-import nipype.interfaces.freesurfer as fs
-from nipype.interfaces.base import File, traits
+from pathlib import Path
+
+from nipype.interfaces import (
+    freesurfer as fs,
+)
+from nipype.interfaces.ants.base import ANTSCommand, ANTSCommandInputSpec
+from nipype.interfaces.base import File, InputMultiObject, TraitedSpec, traits
 
 
 class _MRICoregInputSpec(fs.registration.MRICoregInputSpec):
@@ -23,3 +28,80 @@ class MRICoreg(fs.MRICoreg):
     """
 
     input_spec = _MRICoregInputSpec
+
+
+class ConcatXFMInputSpec(ANTSCommandInputSpec):
+    transforms = InputMultiObject(
+        traits.Either(File(exists=True), 'identity'),
+        argstr='%s',
+        mandatory=True,
+        desc='transform files: will be applied in reverse order. For '
+        'example, the last specified transform will be applied first.',
+    )
+    out_xfm = traits.File(
+        'concat_xfm.h5',
+        usedefault=True,
+        argstr='--output [ %s, 1 ]',
+        desc='output file name',
+    )
+    reference_image = File(
+        argstr='--reference-image %s',
+        mandatory=True,
+        desc='reference image space that you wish to warp INTO',
+        exists=True,
+    )
+    invert_transform_flags = InputMultiObject(traits.Bool())
+
+
+class ConcatXFMOutputSpec(TraitedSpec):
+    out_xfm = File(desc='Combined transform')
+
+
+class ConcatXFM(ANTSCommand):
+    """
+    Streamed use of antsApplyTransforms to combine multiple xfms into a single file
+
+    Examples
+    --------
+
+    >>> from nibabies.interfaces.patches import ConcatXFM
+    >>> cxfm = ConcatXFM()
+    >>> cxfm.inputs.transforms = [testdir / 'xfm0.h5', testdir / 'xfm1.h5']
+    >>> cxfm.inputs.reference_image = testdir / 'anatomical.nii'
+    >>> cxfm.cmdline  # doctest: +ELLIPSIS +NORMALIZE_WHITESPACE
+    'antsApplyTransforms --output [ concat_xfm.h5, 1 ] --reference-image .../anatomical.nii \
+--transform .../xfm0.h5 --transform .../xfm1.h5'
+
+    """
+
+    _cmd = 'antsApplyTransforms'
+    input_spec = ConcatXFMInputSpec
+    output_spec = ConcatXFMOutputSpec
+
+    def _get_transform_filenames(self):
+        retval = []
+        invert_flags = self.inputs.invert_transform_flags
+        if not invert_flags:
+            invert_flags = [False] * len(self.inputs.transforms)
+        elif len(self.inputs.transforms) != len(invert_flags):
+            raise ValueError(
+                'ERROR: The invert_transform_flags list must have the same number '
+                'of entries as the transforms list.'
+            )
+
+        for transform, invert in zip(self.inputs.transforms, invert_flags, strict=False):
+            if invert:
+                retval.append(f'--transform [ {transform}, 1 ]')
+            else:
+                retval.append(f'--transform {transform}')
+        return ' '.join(retval)
+
+    def _format_arg(self, opt, spec, val):
+        if opt == 'transforms':
+            return self._get_transform_filenames()
+        return super()._format_arg(opt, spec, val)
+
+    def _list_outputs(self):
+        outputs = self._outputs().get()
+        outputs['out_xfm'] = Path(self.inputs.out_xfm).absolute()
+        return outputs