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Collect aslref-space CBF derivatives as part of precomputed cache #370

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Collect aslref-space CBF derivatives as part of precomputed cache #370

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65267f2
Start working on precomputed CBF.
tsalo Dec 7, 2023
1cf3ee2
Keep working on precomputed CBF.
tsalo Dec 7, 2023
63d1428
Update.
tsalo Dec 9, 2023
9ff681b
Merge remote-tracking branch 'upstream/main' into precomputed-cbf
tsalo Dec 9, 2023
b2c087d
Merge remote-tracking branch 'upstream/main' into precomputed-cbf
tsalo Dec 14, 2023
f757ac6
Update io_spec.json
tsalo Dec 14, 2023
01c6d64
Test minimal --> full
tsalo Dec 14, 2023
61e31e2
Update base.py
tsalo Dec 14, 2023
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104 changes: 102 additions & 2 deletions aslprep/data/io_spec.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"queries": {
"baseline": {
"hmc": {
"datatype": "func",
"datatype": "perf",
"space": null,
"desc": "hmc",
"suffix": "aslref",
Expand All @@ -12,14 +12,114 @@
]
},
"coreg": {
"datatype": "func",
"datatype": "perf",
"space": null,
"desc": "coreg",
"suffix": "aslref",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf": {
"datatype": "perf",
"space": null,
"desc": null,
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"cbf_ts": {
"datatype": "perf",
"space": null,
"desc": "timeseries",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"att": {
"datatype": "perf",
"space": null,
"desc": null,
"suffix": "att",
"extension": [
".nii.gz",
".nii"
]
},
"cbf_ts_score": {
"datatype": "perf",
"space": null,
"desc": "scoreTimeseries",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf_score": {
"datatype": "perf",
"space": null,
"desc": "score",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf_scrub": {
"datatype": "perf",
"space": null,
"desc": "scrub",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf_basil": {
"datatype": "perf",
"space": null,
"desc": "basil",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf_gm_basil": {
"datatype": "perf",
"space": null,
"desc": "basilGM",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"mean_cbf_wm_basil": {
"datatype": "perf",
"space": null,
"desc": "basilWM",
"suffix": "cbf",
"extension": [
".nii.gz",
".nii"
]
},
"att_basil": {
"datatype": "perf",
"space": null,
"desc": "basil",
"suffix": "att",
"extension": [
".nii.gz",
".nii"
]
}
},
"transforms": {
Expand Down
4 changes: 4 additions & 0 deletions aslprep/tests/data/expected_outputs_test_003_minimal.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -7,10 +7,14 @@ sub-01
sub-01.html
sub-01/ses-1
sub-01/ses-1/perf
sub-01/ses-1/perf/sub-01_ses-1_cbf.json
sub-01/ses-1/perf/sub-01_ses-1_cbf.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-coreg_aslref.json
sub-01/ses-1/perf/sub-01_ses-1_desc-coreg_aslref.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-hmc_aslref.json
sub-01/ses-1/perf/sub-01_ses-1_desc-hmc_aslref.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-timeseries_cbf.json
sub-01/ses-1/perf/sub-01_ses-1_desc-timeseries_cbf.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_from-aslref_to-T1w_mode-image_xfm.json
sub-01/ses-1/perf/sub-01_ses-1_from-aslref_to-T1w_mode-image_xfm.txt
sub-01/ses-1/perf/sub-01_ses-1_from-orig_to-aslref_mode-image_xfm.json
Expand Down
4 changes: 4 additions & 0 deletions aslprep/tests/data/expected_outputs_test_003_resampling.txt
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Original file line number Diff line number Diff line change
Expand Up @@ -8,12 +8,16 @@ sub-01
sub-01.html
sub-01/ses-1
sub-01/ses-1/perf
sub-01/ses-1/perf/sub-01_ses-1_cbf.json
sub-01/ses-1/perf/sub-01_ses-1_cbf.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-confounds_timeseries.tsv
sub-01/ses-1/perf/sub-01_ses-1_desc-coreg_aslref.json
sub-01/ses-1/perf/sub-01_ses-1_desc-coreg_aslref.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-hmc_aslref.json
sub-01/ses-1/perf/sub-01_ses-1_desc-hmc_aslref.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_desc-qualitycontrol_cbf.tsv
sub-01/ses-1/perf/sub-01_ses-1_desc-timeseries_cbf.json
sub-01/ses-1/perf/sub-01_ses-1_desc-timeseries_cbf.nii.gz
sub-01/ses-1/perf/sub-01_ses-1_from-aslref_to-T1w_mode-image_xfm.json
sub-01/ses-1/perf/sub-01_ses-1_from-aslref_to-T1w_mode-image_xfm.txt
sub-01/ses-1/perf/sub-01_ses-1_from-orig_to-aslref_mode-image_xfm.json
Expand Down
18 changes: 16 additions & 2 deletions aslprep/tests/test_cli.py
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Original file line number Diff line number Diff line change
Expand Up @@ -334,6 +334,15 @@ def test_test_003_minimal(data_dir, output_dir, working_dir):
extra_params=["--fs-no-reconall"],
)

base_test_003(
data_dir,
output_dir,
working_dir,
level="full",
level_name="minimal",
extra_params=["--fs-no-reconall"],
)


@pytest.mark.test_003_resampling
def test_test_003_resampling(data_dir, output_dir, working_dir):
Expand All @@ -359,7 +368,7 @@ def test_test_003_full(data_dir, output_dir, working_dir):
)


def base_test_003(data_dir, output_dir, working_dir, level, extra_params):
def base_test_003(data_dir, output_dir, working_dir, level, level_name=None, extra_params=None):
"""Run aslprep on sub-01.

This dataset is Siemens.
Expand All @@ -369,7 +378,11 @@ def base_test_003(data_dir, output_dir, working_dir, level, extra_params):

dataset_dir = download_test_data(TEST_NAME, data_dir)
download_test_data("anatomical", data_dir)
level_test_name = f"{TEST_NAME}_{level}"
if level_name:
level_test_name = f"{TEST_NAME}_{level_name}"
else:
level_test_name = f"{TEST_NAME}_{level}"

out_dir = os.path.join(output_dir, level_test_name, "aslprep")
work_dir = os.path.join(working_dir, level_test_name)

Expand All @@ -383,6 +396,7 @@ def base_test_003(data_dir, output_dir, working_dir, level, extra_params):
"--omp-nthreads=1",
"--output-spaces",
"asl",
"MNI152NLin2009cAsym",
"--use-syn-sdc",
"--m0_scale=10",
f"--fs-subjects-dir={os.path.join(data_dir, 'anatomical/freesurfer')}",
Expand Down
45 changes: 29 additions & 16 deletions aslprep/workflows/asl/base.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,6 +23,7 @@
from aslprep.workflows.asl.fit import init_asl_fit_wf, init_asl_native_wf
from aslprep.workflows.asl.outputs import (
init_ds_asl_native_wf,
init_ds_cbf_native_wf,
init_ds_ciftis_wf,
init_ds_volumes_wf,
)
Expand Down Expand Up @@ -380,6 +381,7 @@ def init_asl_wf(
processing_target=processing_target,
dummy_scans=dummy_scans,
m0_scale=m0_scale,
precomputed=precomputed,
scorescrub=scorescrub,
basil=basil,
smooth_kernel=smooth_kernel,
Expand All @@ -404,6 +406,30 @@ def init_asl_wf(
]),
]) # fmt:skip

# If we want aslref-space outputs, then call the appropriate workflow
aslref_out = bool(nonstd_spaces.intersection(("func", "run", "asl", "aslref", "sbref")))
aslref_out &= config.workflow.level == "full"

# Write out aslref-space CBF derivatives for the minimal and resampling workflows,
# or if we want them anyway.
if (config.workflow.level != "full") or aslref_out:
ds_cbf_native_wf = init_ds_cbf_native_wf(
bids_root=str(config.execution.bids_dir),
output_dir=config.execution.aslprep_dir,
metadata=metadata,
cbf_3d=cbf_3d_derivs,
cbf_4d=cbf_4d_derivs,
att=att_derivs,
)
ds_cbf_native_wf.inputs.inputnode.source_files = [asl_file]

for cbf_deriv in cbf_derivs:
workflow.connect([
(cbf_wf, ds_cbf_native_wf, [
(f"outputnode.{cbf_deriv}", f"inputnode.{cbf_deriv}"),
]),
]) # fmt:skip

if config.workflow.level == "minimal":
return workflow

Expand All @@ -412,7 +438,7 @@ def init_asl_wf(
# - Calculate ASL confounds and CBF QC metrics.
# - Generate plots for CBF.
# - Resample to anatomical space.
# - Save aslref-space outputs only if requested.
# - Save aslref-space ASL outputs only if requested.
#

asl_confounds_wf = init_asl_confounds_wf(
Expand Down Expand Up @@ -482,7 +508,8 @@ def init_asl_wf(
]) # fmt:skip

# Plot CBF outputs.
# NOTE: CIFTI input won't be provided unless level is set to 'full'.
# NOTE: CIFTI input won't be provided unless level is set to 'full' and CIFTI outputs are
# requested.
cbf_reporting_wf = init_cbf_reporting_wf(
metadata=metadata,
plot_timeseries=not (is_multi_pld or use_ge or (config.workflow.level == "resampling")),
Expand Down Expand Up @@ -519,19 +546,12 @@ def init_asl_wf(
(cbf_wf, cbf_reporting_wf, [(f"outputnode.{cbf_deriv}", f"inputnode.{cbf_deriv}")]),
]) # fmt:skip

# If we want aslref-space outputs, then call the appropriate workflow
aslref_out = bool(nonstd_spaces.intersection(("func", "run", "asl", "aslref", "sbref")))
aslref_out &= config.workflow.level == "full"

if aslref_out:
ds_asl_native_wf = init_ds_asl_native_wf(
bids_root=str(config.execution.bids_dir),
output_dir=config.execution.aslprep_dir,
asl_output=aslref_out,
metadata=metadata,
cbf_3d=cbf_3d_derivs,
cbf_4d=cbf_4d_derivs,
att=att_derivs,
)
ds_asl_native_wf.inputs.inputnode.source_files = [asl_file]

Expand All @@ -540,13 +560,6 @@ def init_asl_wf(
(asl_native_wf, ds_asl_native_wf, [("outputnode.asl_native", "inputnode.asl")]),
]) # fmt:skip

for cbf_deriv in cbf_derivs:
workflow.connect([
(cbf_wf, ds_asl_native_wf, [
(f"outputnode.{cbf_deriv}", f"inputnode.{cbf_deriv}"),
]),
]) # fmt:skip

if config.workflow.level == "resampling":
# Fill in datasinks of reportlets seen so far
for node in workflow.list_node_names():
Expand Down
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