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ENH: Add support for ASL data #411

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merged 5 commits into from
Dec 5, 2023
Merged

ENH: Add support for ASL data #411

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844a67b
Add ASL to suffixes.
tsalo Nov 15, 2023
09a0042
Merge remote-tracking branch 'upstream/master' into add-asl
tsalo Dec 1, 2023
e21319e
Add ASL and M0 scan in other locations.
tsalo Dec 1, 2023
6c678d5
Address style issue.
tsalo Dec 1, 2023
3ef588a
Update sdcflows/utils/wrangler.py
tsalo Dec 4, 2023
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10 changes: 7 additions & 3 deletions sdcflows/fieldmaps.py
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Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,8 @@ class EstimatorType(Enum):
"bold": EstimatorType.PEPOLAR,
"dwi": EstimatorType.PEPOLAR,
"epi": EstimatorType.PEPOLAR,
"asl": EstimatorType.PEPOLAR,
"m0scan": EstimatorType.PEPOLAR,
"fieldmap": EstimatorType.MAPPED,
"magnitude": None,
"magnitude1": None,
Expand Down Expand Up @@ -241,7 +243,7 @@ def __attrs_post_init__(self):
self.metadata["TotalReadoutTime"] = 0.0

# Check for REQUIRED metadata (depends on suffix.)
if self.suffix in ("bold", "dwi", "epi", "sbref"):
if self.suffix in ("bold", "dwi", "epi", "sbref", "asl", "m0scan"):
if "PhaseEncodingDirection" not in self.metadata:
raise MetadataError(
f"Missing 'PhaseEncodingDirection' for <{self.path}>."
Expand Down Expand Up @@ -370,10 +372,12 @@ def __attrs_post_init__(self):

# Fieldmap option 2: PEPOLAR (and fieldmap-less or ANAT)
# IMPORTANT NOTE: fieldmap-less approaches can be considered PEPOLAR with RO = 0.0s
pepolar_types = suffix_set.intersection(("bold", "dwi", "epi", "sbref"))
pepolar_types = suffix_set.intersection(("bold", "dwi", "epi", "sbref", "asl", "m0scan"))
anat_types = suffix_set.intersection(("T1w", "T2w"))
_pepolar_estimation = (
len([f for f in suffix_list if f in ("bold", "dwi", "epi", "sbref")]) > 1
len(
[f for f in suffix_list if f in ("bold", "dwi", "epi", "sbref", "asl", "m0scan")]
) > 1
)

if _pepolar_estimation and not anat_types:
Expand Down
15 changes: 8 additions & 7 deletions sdcflows/utils/wrangler.py
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Original file line number Diff line number Diff line change
Expand Up @@ -63,9 +63,9 @@ def find_estimators(
One of more session identifiers. If None, all sessions will be used.
fmapless : :obj:`bool` or :obj:`set`
Indicates if fieldmap-less heuristics should be executed.
When ``fmapless`` is a :obj:`set`, it can contain valid BIDS suffices
for EPI images (namely, ``"dwi"``, ``"bold"``, or ``"sbref"``).
When ``fmapless`` is ``True``, heuristics will use the ``{"bold", "dwi"}`` set.
When ``fmapless`` is a :obj:`set`, it can contain valid BIDS suffixes
for EPI images (namely, ``"dwi"``, ``"bold"``, ``"asl"``, or ``"sbref"``).
When ``fmapless`` is ``True``, heuristics will use the ``{"bold", "dwi", "asl"}`` set.
force_fmapless : :obj:`bool`
When some other fieldmap estimation methods have been found, fieldmap-less
estimation will be skipped except if ``force_fmapless`` is ``True``.
Expand Down Expand Up @@ -306,7 +306,7 @@ def find_estimators(
sessions = sessions or layout.get_sessions(subject=subject) or [None]
fmapless = fmapless or {}
if fmapless is True:
fmapless = {"bold", "dwi"}
fmapless = {"bold", "dwi", "asl"}

estimators = []

Expand Down Expand Up @@ -434,7 +434,7 @@ def find_estimators(
all_targets.append(target)

# If sbrefs are targets, then the goal is generally to estimate with epi+sbref
# and correct bold/dwi
# and correct bold/dwi/asl
sbrefs = [
target for target in all_targets if target.entities["suffix"] == "sbref"
]
Expand All @@ -443,7 +443,7 @@ def find_estimators(
intent_map = []
for sbref in sbrefs:
ents = sbref.get_entities(metadata=False)
ents["suffix"] = ["bold", "dwi"]
ents["suffix"] = ["bold", "dwi", "asl"]
intent_map.append(
[
target
Expand Down Expand Up @@ -540,7 +540,7 @@ def find_anatomical_estimators(
base_entities : :class:`dict`
Entities to use to query for images. These should include any filters.
suffixes : :class:`list`
EPI suffixes, for example ``["bold", "dwi"]``. Associated ``"sbref"``\s
EPI suffixes, for example ``["bold", "dwi", "asl"]``. Associated ``"sbref"``\s
will be found and used in place of BOLD/diffusion EPIs.
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"""

Expand All @@ -555,6 +555,7 @@ def find_anatomical_estimators(
datatype = {
"bold": "func",
"dwi": "dwi",
"asl": "perf",
}[suffix]
candidates = layout.get(
**{
Expand Down
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