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Add --ignore fmap-jacobian option #385

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merged 2 commits into from
Jan 16, 2024
Merged

Add --ignore fmap-jacobian option #385

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3c99647
Add ignore fmap-jacobian option.
tsalo Jan 15, 2024
12faaf2
Update SDCFlows version.
tsalo Jan 15, 2024
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2 changes: 1 addition & 1 deletion aslprep/cli/parser.py
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Original file line number Diff line number Diff line change
Expand Up @@ -242,7 +242,7 @@ def _bids_filter(value):
action="store",
nargs="+",
default=[],
choices=["fieldmaps", "sbref", "t2w", "flair"],
choices=["fieldmaps", "sbref", "t2w", "flair", "fmap-jacobian"],
help=(
"ignore selected aspects of the input dataset to disable corresponding "
"parts of the workflow (a space delimited list)"
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1 change: 1 addition & 0 deletions aslprep/workflows/asl/apply.py
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Expand Up @@ -133,6 +133,7 @@ def init_asl_cifti_resample_wf(
fieldmap_id=fieldmap_id,
omp_nthreads=omp_nthreads,
mem_gb=mem_gb,
jacobian="fmap-jacobian" not in config.workflow.ignore,
name="asl_MNI6_wf",
)

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2 changes: 2 additions & 0 deletions aslprep/workflows/asl/base.py
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Expand Up @@ -563,6 +563,7 @@ def init_asl_wf(
fieldmap_id=fieldmap_id,
omp_nthreads=omp_nthreads,
mem_gb=mem_gb,
jacobian="fmap-jacobian" not in config.workflow.ignore,
name="asl_anat_wf",
)
asl_anat_wf.inputs.inputnode.resolution = "native"
Expand Down Expand Up @@ -626,6 +627,7 @@ def init_asl_wf(
fieldmap_id=fieldmap_id,
omp_nthreads=omp_nthreads,
mem_gb=mem_gb,
jacobian="fmap-jacobian" not in config.workflow.ignore,
name="asl_std_wf",
)
ds_asl_std_wf = init_ds_volumes_wf(
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8 changes: 6 additions & 2 deletions aslprep/workflows/asl/fit.py
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Expand Up @@ -817,7 +817,7 @@ def init_asl_native_wf(

# Resample ASL to aslref
aslref_asl = pe.Node(
ResampleSeries(),
ResampleSeries(jacobian="fmap-jacobian" not in config.workflow.ignore),
name="aslref_asl",
n_procs=omp_nthreads,
mem_gb=mem_gb["resampled"],
Expand Down Expand Up @@ -862,7 +862,11 @@ def init_asl_native_wf(
# No HMC
identity_xfm = nw_data.load("itkIdentityTransform.txt")
aslref_m0scan = pe.Node(
ResampleSeries(transforms=[identity_xfm], in_file=m0scan),
ResampleSeries(
jacobian="fmap-jacobian" not in config.workflow.ignore,
transforms=[identity_xfm],
in_file=m0scan,
),
name="aslref_m0scan",
n_procs=omp_nthreads,
)
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4 changes: 2 additions & 2 deletions pyproject.toml
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Expand Up @@ -18,7 +18,7 @@ license = {file = "LICENSE.md"}
requires-python = ">=3.10"
dependencies = [
'importlib_resources; python_version < "3.11"',
"fmriprep ~= 23.2.0a2",
"fmriprep ~= 23.2.0",
"indexed_gzip >= 0.8.8",
"looseversion",
"networkx ~= 3.2.1", # nipype needs networkx, but 3+ isn"t compatible with nipype 1.8.5
Expand All @@ -32,7 +32,7 @@ dependencies = [
"psutil >= 5.4",
"pybids ~= 0.16.4",
"requests",
"sdcflows ~= 2.7.0",
"sdcflows ~= 2.8.0",
"sentry-sdk >= 0.6.9",
"smriprep ~= 0.13.1",
"templateflow >= 23.0.0",
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