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Merge pull request #415 from mgxd/enh/mni-reg
ENH: Add flag for multi-step registration to adult templates
2 parents b9efa6f + 63afae1 commit b7e3fcc

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-58
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11 files changed

+652
-58
lines changed

‎nibabies/cli/parser.py‎

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

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@@ -578,6 +578,9 @@ class workflow(_Config):
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"""Run FreeSurfer ``recon-all`` with the ``-logitudinal`` flag."""
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medial_surface_nan = None
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"""Fill medial surface with :abbr:`NaNs (not-a-number)` when sampling."""
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multi_step_reg = False
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"""Perform multiple registrations (native -> MNIInfant -> template) and concatenate into a
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single transform"""
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norm_csf = False
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"""Replace low intensity voxels in CSF mask with average."""
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project_goodvoxels = False

‎nibabies/data/xfm_manifest.json‎

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

‎nibabies/interfaces/conftest.py‎

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

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

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