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Merged
merged 21 commits into from
Sep 18, 2025
Merged

Decrease fragility/xcpqc #2277

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14f2da6
:necktie: Make XCPQC inputs optional
shnizzedy Jul 29, 2025
36e7562
:necktie: Group `ICA_AROMA_FSLreg` inputs
shnizzedy Jul 30, 2025
970afa5
:rewind: Revert ":necktie: Group `ICA_AROMA_FSLreg` inputs"
shnizzedy Jul 30, 2025
22df8c3
:loud_sound: Add `new_strats` to verbose logger
shnizzedy Aug 6, 2025
44b0f4b
:loud_sound: Include name when debugging strats
shnizzedy Aug 7, 2025
33bb943
:recycle: Un=daisy-chain registration options
shnizzedy Aug 7, 2025
1d89c09
:truck: `desc-ref_bold` → `sbref`
shnizzedy Aug 8, 2025
5d9dafc
:goal_net: Try to short-circuit crossed streams
shnizzedy Aug 8, 2025
1b6bd2e
:necktie: Move short-circuit
shnizzedy Aug 9, 2025
2bff2a5
:white_check_mark: Update `brain_mask_freesurfer_fsl` tests
shnizzedy Aug 11, 2025
33756d2
:loud_sound: Improve dropped variant logging
shnizzedy Aug 13, 2025
5376cf3
:recycle: Reduce initial number of connections; fix short-circuit
shnizzedy Aug 26, 2025
1a4c8d9
:recycle: Restore consecutive forking ability
shnizzedy Aug 29, 2025
cc5648e
:rewind: Revert ":recycle: Restore consecutive forking ability"
shnizzedy Sep 2, 2025
9c551be
:necktie: Stringify variants to handle chains
shnizzedy Sep 2, 2025
bac897f
:twisted_rightwards_arrows: Merge branch 'develop' into 'decrease-fra…
shnizzedy Sep 11, 2025
5a48533
adding match fov node to convert fs brain mask to native space
birajstha Sep 11, 2025
1df0639
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Sep 11, 2025
5196fe4
bringing the FS brain mask to T1 space before anat skull stripping (#…
shnizzedy Sep 12, 2025
dcf6063
:twisted_rightwards_arrows: Merge branch 'develop' into 'decrease-fra…
shnizzedy Sep 15, 2025
ee00500
Merge branch 'develop' into decrease-fragility/xcpqc
shnizzedy Sep 18, 2025
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308 changes: 103 additions & 205 deletions CPAC/anat_preproc/anat_preproc.py
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Original file line number Diff line number Diff line change
Expand Up @@ -28,7 +28,6 @@
fsl_aff_to_rigid,
fslmaths_command,
mri_convert,
normalize_wmparc,
pad,
VolumeRemoveIslands,
wb_command,
Expand Down Expand Up @@ -696,13 +695,15 @@ def afni_brain_connector(wf, cfg, strat_pool, pipe_num, opt):

wf.connect(anat_skullstrip, "out_file", anat_brain_mask, "in_file_a")

outputs = {}

if strat_pool.check_rpool("desc-preproc_T1w"):
outputs = {"space-T1w_desc-brain_mask": (anat_brain_mask, "out_file")}

elif strat_pool.check_rpool("desc-preproc_T2w"):
outputs = {"space-T2w_desc-brain_mask": (anat_brain_mask, "out_file")}

return (wf, outputs)
return wf, outputs


def fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):
Expand Down Expand Up @@ -1322,22 +1323,29 @@ def freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt):

wf.connect(combine_mask, "out_file", binarize_combined_mask, "in_file")

if opt == "FreeSurfer-BET-Tight":
outputs = {
"space-T1w_desc-tight_brain_mask": (
binarize_combined_mask,
"out_file",
)
}
elif opt == "FreeSurfer-BET-Loose":
outputs = {
"space-T1w_desc-loose_brain_mask": (
binarize_combined_mask,
"out_file",
)
}
# CCS brain mask is in FS space, transfer it back to native T1 space
match_fov_ccs_brain_mask = pe.Node(
interface=fsl.FLIRT(), name=f"match_fov_CCS_brain_mask_{node_id}"
)
match_fov_ccs_brain_mask.inputs.apply_xfm = True
match_fov_ccs_brain_mask.inputs.uses_qform = True
match_fov_ccs_brain_mask.inputs.interp = "nearestneighbour"

return (wf, outputs)
node, out = strat_pool.get_data("pipeline-fs_raw-average")
convert_fs_T1_to_nifti = pe.Node(
Function(
input_names=["in_file"], output_names=["out_file"], function=mri_convert
),
name=f"convert_fs_T1_to_nifti_for_ccs_{node_id}",
)
wf.connect(node, out, convert_fs_T1_to_nifti, "in_file")
wf.connect(
convert_fs_T1_to_nifti, "out_file", match_fov_ccs_brain_mask, "reference"
)

wf.connect(binarize_combined_mask, "out_file", match_fov_ccs_brain_mask, "in_file")

return wf, {"space-T1w_desc-brain_mask": (match_fov_ccs_brain_mask, "out_file")}


def mask_T2(wf_name="mask_T2"):
Expand Down Expand Up @@ -1408,9 +1416,8 @@ def mask_T2(wf_name="mask_T2"):
)
def anatomical_init(wf, cfg, strat_pool, pipe_num, opt=None):
if opt not in anatomical_init.option_val:
raise ValueError(
f"\n[!] Error: Invalid option for deoblique: {opt}. \nExpected one of {anatomical_init.option_val}"
)
msg = f"\n[!] Error: Invalid option for deoblique: {opt}. \nExpected one of {anatomical_init.option_val}"
raise ValueError(msg)

if opt == "warp":
anat_deoblique = pe.Node(
Expand Down Expand Up @@ -1500,15 +1507,15 @@ def acpc_align_head(wf, cfg, strat_pool, pipe_num, opt=None):
(
"desc-head_T1w",
"desc-preproc_T1w",
["space-T1w_desc-brain_mask", "space-T1w_desc-brain_mask"],
"space-T1w_desc-brain_mask",
),
"T1w-ACPC-template",
"T1w-brain-ACPC-template",
],
outputs=[
"desc-head_T1w",
"desc-preproc_T1w",
["space-T1w_desc-brain_mask", "space-T1w_desc-brain_mask"],
"space-T1w_desc-brain_mask",
"from-T1w_to-ACPC_mode-image_desc-aff2rig_xfm",
],
)
Expand Down Expand Up @@ -1939,211 +1946,102 @@ def brain_mask_acpc_unet(wf, cfg, strat_pool, pipe_num, opt=None):
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-Brainmask",
inputs=[
"pipeline-fs_raw-average",
"pipeline-fs_brainmask",
"freesurfer-subject-dir",
option_val=[
"FreeSurfer-ABCD",
"FreeSurfer-BET-Loose",
"FreeSurfer-BET-Tight",
"FreeSurfer-Brainmask",
],
outputs=["space-T1w_desc-brain_mask"],
)
def brain_mask_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
wf, outputs = freesurfer_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

return (wf, outputs)


@nodeblock(
name="brain_mask_acpc_freesurfer",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-Brainmask",
inputs=[
"space-T1w_desc-brain_mask",
"pipeline-fs_raw-average",
"freesurfer-subject-dir",
],
outputs=["space-T1w_desc-acpcbrain_mask"],
)
def brain_mask_acpc_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
wf, wf_outputs = freesurfer_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

outputs = {"space-T1w_desc-acpcbrain_mask": wf_outputs["space-T1w_desc-brain_mask"]}

return (wf, outputs)


@nodeblock(
name="brain_mask_freesurfer_abcd",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-ABCD",
inputs=[
["desc-restore_T1w", "desc-preproc_T1w"],
"pipeline-fs_wmparc",
"pipeline-fs_raw-average",
"freesurfer-subject-dir",
],
outputs=["space-T1w_desc-brain_mask"],
)
def brain_mask_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
wf, outputs = freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

return (wf, outputs)


@nodeblock(
name="brain_mask_freesurfer_fsl_tight",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-BET-Tight",
inputs=[
"pipeline-fs_brainmask",
"pipeline-fs_T1",
"pipeline-fs_raw-average",
"freesurfer-subject-dir",
(
["desc-restore_T1w", "desc-preproc_T1w"],
"space-T1w_desc-brain_mask",
"pipeline-fs_T1",
"pipeline-fs_wmparc",
"pipeline-fs_raw-average",
"pipeline-fs_brainmask",
"freesurfer-subject-dir",
),
"T1w-brain-template-mask-ccs",
"T1w-ACPC-template",
],
outputs={
"space-T1w_desc-brain_mask": {
"Description": "Brain mask extracted using FreeSurfer-BET-Tight method",
"Method": "FreeSurfer-BET-Tight",
"Threshold": "tight",
}
},
outputs={"space-T1w_desc-brain_mask": {}},
)
def brain_mask_freesurfer_fsl_tight(wf, cfg, strat_pool, pipe_num, opt=None):
wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

# Convert the tight brain mask to generic brain mask
outputs["space-T1w_desc-brain_mask"] = outputs.pop(
"space-T1w_desc-tight_brain_mask"
)
return (wf, outputs)
def brain_mask_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
assert isinstance(brain_mask_freesurfer.outputs, dict)
brain_mask_freesurfer.outputs["space-T1w_desc-brain_mask"] = {
"Description": f"Brain mask extracted using {opt} method",
"Method": opt,
}
match opt:
case "FreeSurfer-ABCD":
return freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
case "FreeSurfer-BET-Loose" | "FreeSurfer-BET-Tight":
brain_mask_freesurfer.outputs["space-T1w_desc-brain_mask"]["Threshold"] = (
opt.rsplit("-")[-1].lower()
)
return freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
case "FreeSurfer-Brainmask":
return freesurfer_brain_connector(wf, cfg, strat_pool, pipe_num, opt)
return wf, {}


@nodeblock(
name="brain_mask_acpc_freesurfer_abcd",
name="brain_mask_acpc_freesurfer",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-ABCD",
inputs=[
["desc-restore_T1w", "desc-preproc_T1w"],
"pipeline-fs_wmparc",
"pipeline-fs_raw-average",
"freesurfer-subject-dir",
],
outputs=["space-T1w_desc-acpcbrain_mask"],
)
def brain_mask_acpc_freesurfer_abcd(wf, cfg, strat_pool, pipe_num, opt=None):
wf, wf_outputs = freesurfer_abcd_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

outputs = {"space-T1w_desc-acpcbrain_mask": wf_outputs["space-T1w_desc-brain_mask"]}

return (wf, outputs)


@nodeblock(
name="brain_mask_freesurfer_fsl_loose",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
option_val=[
"FreeSurfer-ABCD",
"FreeSurfer-Brainmask",
"FreeSurfer-BET-Loose",
"FreeSurfer-BET-Tight",
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-BET-Loose",
inputs=[
"pipeline-fs_brainmask",
"pipeline-fs_T1",
"pipeline-fs_raw-average",
"freesurfer-subject-dir",
"T1w-brain-template-mask-ccs",
"T1w-ACPC-template",
],
outputs={
"space-T1w_desc-brain_mask": {
"Description": "Brain mask extracted using FreeSurfer-BET-Loose method",
"Method": "FreeSurfer-BET-Loose",
"Threshold": "loose",
}
},
)
def brain_mask_freesurfer_fsl_loose(wf, cfg, strat_pool, pipe_num, opt=None):
wf, outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

# Convert the loose brain mask to generic brain mask
outputs["space-T1w_desc-brain_mask"] = outputs.pop(
"space-T1w_desc-loose_brain_mask"
)
return (wf, outputs)


@nodeblock(
name="brain_mask_acpc_freesurfer_fsl_tight",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-BET-Tight",
inputs=[
"pipeline-fs_brainmask",
"pipeline-fs_T1",
"T1w-brain-template-mask-ccs",
(
["desc-restore_T1w", "desc-preproc_T1w"],
"space-T1w_desc-brain_mask",
"space-T1w_desc-acpcbrain_mask",
"pipeline-fs_brainmask",
"pipeline-fs_raw-average",
"pipeline-fs_T1",
"pipeline-fs_wmparc",
"freesurfer-subject-dir",
),
"T1w-ACPC-template",
],
outputs=["space-T1w_desc-tight_acpcbrain_mask"],
)
def brain_mask_acpc_freesurfer_fsl_tight(wf, cfg, strat_pool, pipe_num, opt=None):
wf, wf_outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

outputs = {
"space-T1w_desc-tight_acpcbrain_mask": wf_outputs[
"space-T1w_desc-tight_brain_mask"
]
}

return (wf, outputs)


@nodeblock(
name="brain_mask_acpc_freesurfer_fsl_loose",
switch=[
["anatomical_preproc", "brain_extraction", "run"],
["anatomical_preproc", "run"],
],
option_key=["anatomical_preproc", "brain_extraction", "using"],
option_val="FreeSurfer-BET-Loose",
inputs=[
"pipeline-fs_brainmask",
"pipeline-fs_T1",
"T1w-brain-template-mask-ccs",
"T1w-ACPC-template",
],
outputs=["space-T1w_desc-loose_acpcbrain_mask"],
outputs={"space-T1w_desc-acpcbrain_mask": {}},
)
def brain_mask_acpc_freesurfer_fsl_loose(wf, cfg, strat_pool, pipe_num, opt=None):
wf, wf_outputs = freesurfer_fsl_brain_connector(wf, cfg, strat_pool, pipe_num, opt)

outputs = {
"space-T1w_desc-loose_acpcbrain_mask": wf_outputs[
"space-T1w_desc-loose_brain_mask"
]
def brain_mask_acpc_freesurfer(wf, cfg, strat_pool, pipe_num, opt=None):
if opt != strat_pool.get_json("space-T1w_desc-brain_mask").get(
"CpacVariant", {}
).get("space-T1w_mask", opt):
# https://tenor.com/baIhQ.gif
return wf, {}
assert isinstance(brain_mask_acpc_freesurfer.outputs, dict)
outputs = wf_outputs = {}
key = "space-T1w_desc-brain_mask"
functions = {
"FreeSurfer-ABCD": freesurfer_abcd_brain_connector,
"FreeSurfer-Brainmask": freesurfer_brain_connector,
"FreeSurfer-BET-Loose": freesurfer_fsl_brain_connector,
"FreeSurfer-BET-Tight": freesurfer_fsl_brain_connector,
}
if opt in ["FreeSurfer-BET-Loose", "FreeSurfer-BET-Tight"]:
brain_mask_acpc_freesurfer.outputs["space-T1w_desc-acpcbrain_mask"] = {
"Description": f"Brain mask extracted using {opt} method",
"Method": opt,
"Threshold": opt.rsplit("-")[-1].lower(),
}
if opt in functions:
wf, wf_outputs = functions[opt](wf, cfg, strat_pool, pipe_num, opt)
if key in wf_outputs:
outputs = {"space-T1w_desc-acpcbrain_mask": wf_outputs[key]}

return (wf, outputs)
return wf, outputs


@nodeblock(
Expand Down
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