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Merge pull request #370 from effigies/enh/fit-msmsulc
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ENH: Add sphere registration to fit workflow, check for precomputed
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@effigies
effigies authored Oct 11, 2023
2 parents f6b842f + 3b5b230 commit 92773f5
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Showing 8 changed files with 449 additions and 267 deletions.
6 changes: 6 additions & 0 deletions .circleci/config.yml
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Expand Up @@ -12,6 +12,9 @@ _machine_defaults: &machine_defaults
_python_defaults: &python_defaults
docker:
- image: cimg/python:3.10.9
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/src/smriprep

_docker_auth: &docker_auth
Expand Down Expand Up @@ -43,6 +46,9 @@ _pull_from_registry: &pull_from_registry
docs_deploy: &docs
docker:
- image: node:8.10.0
auth:
username: $DOCKER_USER
password: $DOCKER_PAT
working_directory: /tmp/gh-pages
steps:
- run:
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3 changes: 3 additions & 0 deletions .circleci/ds005_outputs.txt
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Expand Up @@ -16,6 +16,7 @@ smriprep/sub-01/anat/sub-01_desc-brain_mask.json
smriprep/sub-01/anat/sub-01_desc-brain_mask.nii.gz
smriprep/sub-01/anat/sub-01_desc-preproc_T1w.json
smriprep/sub-01/anat/sub-01_desc-preproc_T1w.nii.gz
smriprep/sub-01/anat/sub-01_desc-ribbon_mask.json
smriprep/sub-01/anat/sub-01_desc-ribbon_mask.nii.gz
smriprep/sub-01/anat/sub-01_dseg.nii.gz
smriprep/sub-01/anat/sub-01_from-fsnative_to-T1w_mode-image_xfm.txt
Expand All @@ -27,6 +28,7 @@ smriprep/sub-01/anat/sub-01_hemi-L_midthickness.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_pial.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-msmsulc_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_space-fsLR_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-L_sulc.shape.gii
smriprep/sub-01/anat/sub-01_hemi-L_thickness.shape.gii
smriprep/sub-01/anat/sub-01_hemi-L_white.surf.gii
Expand All @@ -37,6 +39,7 @@ smriprep/sub-01/anat/sub-01_hemi-R_midthickness.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_pial.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-msmsulc_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_space-fsLR_desc-reg_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_sphere.surf.gii
smriprep/sub-01/anat/sub-01_hemi-R_sulc.shape.gii
smriprep/sub-01/anat/sub-01_hemi-R_thickness.shape.gii
smriprep/sub-01/anat/sub-01_hemi-R_white.surf.gii
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105 changes: 64 additions & 41 deletions smriprep/data/io_spec.json
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Expand Up @@ -70,68 +70,91 @@
"mode": "image"
}
},
"std_xfms": {
"anat2std_xfm": {
"surfaces": {
"white": {
"datatype": "anat",
"extension": "h5",
"from": "T1w",
"to": [],
"suffix": "xfm",
"mode": "image"
"hemi": ["L", "R"],
"space": null,
"suffix": "white",
"extension": ".surf.gii"
},
"std2anat_xfm": {
"pial": {
"datatype": "anat",
"extension": "h5",
"from": [],
"to": "T1w",
"suffix": "xfm",
"mode": "image"
}
},
"surfaces": {
"t1w_aseg": {
"hemi": ["L", "R"],
"space": null,
"suffix": "pial",
"extension": ".surf.gii"
},
"midthickness": {
"datatype": "anat",
"desc": "aseg",
"suffix": "dseg"
"hemi": ["L", "R"],
"space": null,
"suffix": "midthickness",
"extension": ".surf.gii"
},
"t1w_aparc": {
"sphere": {
"datatype": "anat",
"desc": "aparcaseg",
"suffix": "dseg"
"hemi": ["L", "R"],
"space": null,
"desc": null,
"suffix": "sphere",
"extension": ".surf.gii"
},
"t1w2fsnative_xfm": {
"thickness": {
"datatype": "anat",
"from": "T1w",
"to": "fsnative",
"extension": "txt",
"suffix": "xfm",
"mode": "image"
"hemi": ["L", "R"],
"space": null,
"suffix": "thickness",
"extension": ".shape.gii"
},
"fsnative2t1w_xfm": {
"sulc": {
"datatype": "anat",
"from": "fsnative",
"to": "T1w",
"extension": "txt",
"suffix": "xfm",
"mode": "image"
"hemi": ["L", "R"],
"space": null,
"suffix": "sulc",
"extension": ".shape.gii"
},
"surfaces": {
"curv": {
"datatype": "anat",
"hemi": ["L", "R"],
"extension": "surf.gii",
"suffix": [ "inflated", "midthickness", "pial", "white"]
"space": null,
"suffix": "curv",
"extension": ".shape.gii"
},
"morphometrics": {
"sphere_reg": {
"datatype": "anat",
"hemi": ["L", "R"],
"extension": "shape.gii",
"suffix": ["thickness", "sulc", "curv"]
"space": null,
"desc": "reg",
"suffix": "sphere",
"extension": ".surf.gii"
},
"sphere_reg_fsLR": {
"datatype": "anat",
"hemi": ["L", "R"],
"space": "fsLR",
"desc": "reg",
"suffix": "sphere",
"extension": ".surf.gii"
},
"sphere_reg_msm": {
"datatype": "anat",
"hemi": ["L", "R"],
"space": "fsLR",
"desc": "msmsulc",
"suffix": "sphere",
"extension": ".surf.gii"
}
},
"masks": {
"anat_ribbon": {
"datatype": "anat",
"desc": "ribbon",
"suffix": "mask",
"extension": "nii.gz"
"extension": [
".nii.gz",
".nii"
]
}
}
},
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76 changes: 8 additions & 68 deletions smriprep/utils/bids.py
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Expand Up @@ -21,39 +21,13 @@
# https://www.nipreps.org/community/licensing/
#
"""Utilities to handle BIDS inputs."""
from collections import defaultdict
from pathlib import Path
from json import loads
from pkg_resources import resource_filename as pkgrf
from bids.layout import BIDSLayout
from bids.layout.writing import build_path


def get_outputnode_spec():
"""
Generate outputnode's fields from I/O spec file.
Examples
--------
>>> get_outputnode_spec() # doctest: +NORMALIZE_WHITESPACE
['t1w_preproc', 't1w_mask', 't1w_dseg', 't1w_tpms',
'std_preproc', 'std_mask', 'std_dseg', 'std_tpms',
'anat2std_xfm', 'std2anat_xfm',
't1w_aseg', 't1w_aparc',
't1w2fsnative_xfm', 'fsnative2t1w_xfm',
'surfaces', 'morphometrics', 'anat_ribbon']
"""
spec = loads(Path(pkgrf("smriprep", "data/io_spec.json")).read_text())["queries"]
fields = ["_".join((m, s)) for m in ("t1w", "std") for s in spec["baseline"].keys()]
fields += [s for s in spec["std_xfms"].keys()]
fields += [s for s in spec["surfaces"].keys()]
return fields


def collect_derivatives(
derivatives_dir, subject_id, std_spaces, freesurfer, spec=None, patterns=None
):
def collect_derivatives(derivatives_dir, subject_id, std_spaces, spec=None, patterns=None):
"""Gather existing derivatives and compose a cache."""
if spec is None or patterns is None:
_spec, _patterns = tuple(
Expand All @@ -65,27 +39,9 @@ def collect_derivatives(
if patterns is None:
patterns = _patterns

derivs_cache = defaultdict(list, {})
layout = BIDSLayout(derivatives_dir, config=["bids", "derivatives"], validate=False)
derivatives_dir = Path(derivatives_dir)

def _check_item(item):
if not item:
return None

if isinstance(item, str):
item = [item]

result = []
for i in item:
if not (derivatives_dir / i).exists():
i = i.rstrip(".gz")
if not (derivatives_dir / i).exists():
return None
result.append(str(derivatives_dir / i))

return result

derivs_cache = {}
for k, q in spec["baseline"].items():
q["subject"] = subject_id
item = layout.get(return_type='filename', **q)
Expand All @@ -94,18 +50,6 @@ def _check_item(item):

derivs_cache["t1w_%s" % k] = item[0] if len(item) == 1 else item

for space in std_spaces:
for k, q in spec["std_xfms"].items():
q["subject"] = subject_id
q["from"] = q["from"] or space
q["to"] = q["to"] or space
item = layout.get(return_type='filename', **q)
if not item:
continue
derivs_cache[k] += item

derivs_cache = dict(derivs_cache) # Back to a standard dictionary

transforms = derivs_cache.setdefault('transforms', {})
for space in std_spaces:
for k, q in spec["transforms"].items():
Expand All @@ -118,18 +62,14 @@ def _check_item(item):
continue
transforms.setdefault(space, {})[k] = item[0] if len(item) == 1 else item

if freesurfer:
for k, q in spec["surfaces"].items():
q["subject"] = subject_id
item = _check_item(build_path(q, patterns))
if not item:
continue
for k, q in spec["surfaces"].items():
q["subject"] = subject_id
item = layout.get(return_type='filename', **q)
if not item or len(item) != 2:
continue

if len(item) == 1:
item = item[0]
derivs_cache[k] = item
derivs_cache[k] = sorted(item)

derivs_cache["template"] = std_spaces
return derivs_cache


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