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🔀 Merge branch 'develop' into 'prep_for/mri_robust_template'
2 parents 3ed8c3d + 2567db5 commit 6650c72

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‎CHANGELOG.md‎

Lines changed: 6 additions & 5 deletions
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@@ -43,7 +43,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- Renamed `desc-ref_bold` created in this workflow to `desc-unifized_bold`.
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- `coregistration_prep_fmriprep` nodeblock now checks if `desc-unifized_bold` exists in the Resource Pool, if not it runs the `FSL-AFNI subworkflow` to create it.
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- Input `desc-brain_bold` to `desc-preproc_bold` for `sbref` generation nodeblock `coregistration_prep_vol`.
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- Disabled variant image builds.
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- Turned `generate_xcpqc_files` on for all preconfigurations except `blank`.
47+
- Introduced specific switch `restore_t1w_intensity` for `correct_restore_brain_intensity_abcd` nodeblock, enabling it by default only in `abcd-options` pre-config.
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### Fixed
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@@ -69,6 +70,10 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- `input` field from `coregistration` in blank and default config.
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- `reg_with_skull` swtich from `func_input_prep` in blank and default config.
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73+
#### Removed CI dependency
74+
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- `tj-actions/changed-files` ([CVE-2023-51664](https://www.stepsecurity.io/blog/harden-runner-detection-tj-actions-changed-files-action-is-compromised))
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## [1.8.7] - 2024-05-03
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### Added
@@ -140,10 +145,6 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- `wxpython`
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- `yamlordereddictloader`
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#### Removed CI dependency
144-
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- `tj-actions/changed-files` ([CVE-2023-51664](https://www.stepsecurity.io/blog/harden-runner-detection-tj-actions-changed-files-action-is-compromised))
146-
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### Upgraded dependencies
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- `AFNI` 21.1.00 'Domitian' → 23.3.09 'Septimius Severus'

‎CPAC/anat_preproc/anat_preproc.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -3161,9 +3161,8 @@ def fast_bias_field_correction(config=None, wf_name="fast_bias_field_correction"
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@nodeblock(
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name="correct_restore_brain_intensity_abcd",
3164-
config=["anatomical_preproc", "brain_extraction"],
3165-
option_key="using",
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option_val="FreeSurfer-ABCD",
3164+
config=["anatomical_preproc", "restore_t1w_intensity"],
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switch=["run"],
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inputs=[
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(
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"desc-preproc_T1w",

‎CPAC/pipeline/schema.py‎

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Original file line numberDiff line numberDiff line change
@@ -639,6 +639,9 @@ def sanitize(filename):
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},
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"FreeSurfer-BET": {"T1w_brain_template_mask_ccs": Maybe(str)},
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},
642+
"restore_t1w_intensity": {
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"run": bool1_1,
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},
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},
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"segmentation": {
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"run": bool1_1,

‎CPAC/registration/registration.py‎

Lines changed: 22 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -1601,7 +1601,7 @@ def FSL_registration_connector(
16011601
fnirt_reg_anat_mni,
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"outputspec.output_head",
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),
1604-
f"space-{sym}template_desc-{orig}_mask": (
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f"space-{sym}template_desc-{'brain' if orig == 'T1w' else orig}_mask": (
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fnirt_reg_anat_mni,
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"outputspec.output_mask",
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),
@@ -2318,26 +2318,28 @@ def register_FSL_anat_to_template(wf, cfg, strat_pool, pipe_num, opt=None):
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"dilated-symmetric-brain-mask",
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],
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outputs={
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"space-symtemplate_desc-preproc_T1w": {
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"Template": "T1w-brain-template-symmetric"
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},
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"from-T1w_to-symtemplate_mode-image_desc-linear_xfm": {
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"Template": "T1w-template-symmetric"
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},
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"from-symtemplate_to-T1w_mode-image_desc-linear_xfm": {
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"Template": "T1w-template-symmetric"
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},
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"from-T1w_to-symtemplate_mode-image_xfm": {
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"Template": "T1w-template-symmetric"
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},
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"from-longitudinal_to-symtemplate_mode-image_desc-linear_xfm": {
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"Template": "T1w-template-symmetric"
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},
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"from-symtemplate_to-longitudinal_mode-image_desc-linear_xfm": {
2337-
"Template": "T1w-template-symmetric"
2321+
**{
2322+
f"space-symtemplate_desc-{suffix}": {
2323+
"Template": "T1w-brain-template-symmetric"
2324+
}
2325+
for suffix in [
2326+
*[f"{desc}_T1w" for desc in ["brain", "preproc"]],
2327+
"brain_mask",
2328+
]
23382329
},
2339-
"from-longitudinal_to-symtemplate_mode-image_xfm": {
2340-
"Template": "T1w-template-symmetric"
2330+
**{
2331+
output: {"Template": "T1w-template-symmetric"}
2332+
for output in [
2333+
"space-symtemplate_desc-head_T1w",
2334+
"from-T1w_to-symtemplate_mode-image_desc-linear_xfm",
2335+
"from-symtemplate_to-T1w_mode-image_desc-linear_xfm",
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"from-T1w_to-symtemplate_mode-image_warp",
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"from-T1w_to-symtemplate_mode-image_xfm",
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"from-longitudinal_to-symtemplate_mode-image_desc-linear_xfm",
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"from-symtemplate_to-longitudinal_mode-image_desc-linear_xfm",
2340+
"from-longitudinal_to-symtemplate_mode-image_xfm",
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"space-symtemplate_desc-T1wT2w_biasfield",
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]
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},
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},
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)

‎CPAC/resources/configs/pipeline_config_abcd-options.yml‎

Lines changed: 11 additions & 1 deletion
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@@ -13,6 +13,14 @@ pipeline_setup:
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# Name for this pipeline configuration - useful for identification.
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# This string will be sanitized and used in filepaths
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pipeline_name: cpac_abcd-options
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output_directory:
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# Quality control outputs
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quality_control:
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# Generate eXtensible Connectivity Pipeline-style quality control files
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generate_xcpqc_files: On
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system_config:
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# The maximum amount of memory each participant's workflow can allocate.
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# this is a fork option
8189
using: [FreeSurfer-ABCD]
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91+
restore_t1w_intensity:
92+
run: On
93+
8394
# Non-local means filtering via ANTs DenoiseImage
8495
non_local_means_filtering:
8596

@@ -203,7 +214,6 @@ registration_workflows:
203214
# input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
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input: [Selected_Functional_Volume]
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206-
#TODO Add input field here to choose between whole head or brain
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# Choose coregistration interpolation
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interpolation: spline
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‎CPAC/resources/configs/pipeline_config_abcd-prep.yml‎

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@@ -13,6 +13,14 @@ pipeline_setup:
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# Name for this pipeline configuration - useful for identification.
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# This string will be sanitized and used in filepaths
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pipeline_name: cpac_abcd-prep
16+
output_directory:
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18+
# Quality control outputs
19+
quality_control:
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# Generate eXtensible Connectivity Pipeline-style quality control files
22+
generate_xcpqc_files: On
23+
1624
system_config:
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1826
# The maximum amount of memory each participant's workflow can allocate.
@@ -167,7 +175,6 @@ registration_workflows:
167175
# input: ['Mean_Functional', 'Selected_Functional_Volume', 'fmriprep_reference']
168176
input: [Selected_Functional_Volume]
169177

170-
#TODO Add input field here to choose between whole head or brain
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# Choose coregistration interpolation
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interpolation: spline
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‎CPAC/resources/configs/pipeline_config_benchmark-ANTS.yml‎

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@@ -18,6 +18,9 @@ pipeline_setup:
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# Quality control outputs
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quality_control:
2020

21+
# Generate eXtensible Connectivity Pipeline-style quality control files
22+
generate_xcpqc_files: On
23+
2124
# Generate quality control pages containing preprocessing and derivative outputs.
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generate_quality_control_images: On
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‎CPAC/resources/configs/pipeline_config_benchmark-FNIRT.yml‎

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@@ -18,6 +18,9 @@ pipeline_setup:
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# Quality control outputs
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quality_control:
2020

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# Generate eXtensible Connectivity Pipeline-style quality control files
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generate_xcpqc_files: On
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# Generate quality control pages containing preprocessing and derivative outputs.
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generate_quality_control_images: On
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‎CPAC/resources/configs/pipeline_config_blank.yml‎

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Original file line numberDiff line numberDiff line change
@@ -419,6 +419,9 @@ anatomical_preproc:
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# niworkflows-ants registration mask (can be optional)
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regmask_path: /ants_template/oasis/T_template0_BrainCerebellumRegistrationMask.nii.gz
421421

422+
restore_t1w_intensity:
423+
run: Off
424+
422425
run_t2: Off
423426

424427
# Bias field correction based on square root of T1w * T2w
@@ -747,7 +750,6 @@ registration_workflows:
747750
# Choose FSL or ABCD as coregistration method
748751
using: FSL
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750-
#TODO Add input field here to choose between whole head or brain
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# Choose coregistration interpolation
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interpolation: trilinear
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‎CPAC/resources/configs/pipeline_config_ccs-options.yml‎

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@@ -18,6 +18,9 @@ pipeline_setup:
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# Quality control outputs
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quality_control:
2020

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# Generate eXtensible Connectivity Pipeline-style quality control files
22+
generate_xcpqc_files: On
23+
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# Generate quality control pages containing preprocessing and derivative outputs.
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generate_quality_control_images: On
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