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🚚 ref_mask_res-2 and T1w_template_res-2 fields are moved out of regis… #2178

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Merged
merged 5 commits into from
Feb 5, 2025
Merged

🚚 ref_mask_res-2 and T1w_template_res-2 fields are moved out of regis… #2178

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1a6c9dc
🚚 ref_mask_res-2 and T1w_template_res-2 fields are moved out of regis…
birajstha Jan 28, 2025
75612ae
🚚 moving ref_mask_res-2 and T1w_template_res-2 from default and fmrip…
birajstha Jan 28, 2025
6d65824
🦺 pushing with pre-commit
birajstha Jan 28, 2025
725b1de
Merge branch 'develop' into abcd-prep
birajstha Jan 30, 2025
01d0602
Merge branch 'develop' into abcd-prep
birajstha Feb 5, 2025
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1 change: 1 addition & 0 deletions CHANGELOG.md
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Expand Up @@ -30,6 +30,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- Moved `pygraphviz` from requirements to `graphviz` optional dependencies group.
- Automatically tag untagged `subject_id` and `unique_id` as `!!str` when loading data config files.
- Made orientation configurable (was hard-coded as "RPI").
- Moved `ref_mask_res_2` and `T1w_template_res-2` fields from registration into surface under `abcd_prefreesurfer_prep`.

### Fixed

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4 changes: 2 additions & 2 deletions CPAC/pipeline/schema.py
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Expand Up @@ -712,8 +712,6 @@ def sanitize(filename):
"interpolation": In({"trilinear", "sinc", "spline"}),
"identity_matrix": Maybe(str),
"ref_mask": Maybe(str),
"ref_mask_res-2": Maybe(str),
"T1w_template_res-2": Maybe(str),
},
},
"overwrite_transform": {
Expand Down Expand Up @@ -816,6 +814,8 @@ def sanitize(filename):
"surface_analysis": {
"abcd_prefreesurfer_prep": {
"run": bool1_1,
"ref_mask_res-2": Maybe(str),
"T1w_template_res-2": Maybe(str),
},
"freesurfer": {
"run_reconall": bool1_1,
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13 changes: 6 additions & 7 deletions CPAC/resources/configs/pipeline_config_abcd-options.yml
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Expand Up @@ -32,6 +32,12 @@ surface_analysis:
abcd_prefreesurfer_prep:
run: On

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz

# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
Expand Down Expand Up @@ -102,13 +108,6 @@ registration_workflows:
anatomical_registration:
run: On
registration:
FSL-FNIRT:

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz

# option parameters
ANTs:
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13 changes: 6 additions & 7 deletions CPAC/resources/configs/pipeline_config_abcd-prep.yml
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Expand Up @@ -32,6 +32,12 @@ surface_analysis:
abcd_prefreesurfer_prep:
run: On

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz

anatomical_preproc:
run: On
acpc_alignment:
Expand Down Expand Up @@ -72,13 +78,6 @@ anatomical_preproc:
registration_workflows:
anatomical_registration:
registration:
FSL-FNIRT:

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: /opt/dcan-tools/pipeline/global/templates/MNI152_T1_2mm.nii.gz

# option parameters
ANTs:
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12 changes: 6 additions & 6 deletions CPAC/resources/configs/pipeline_config_blank.yml
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Expand Up @@ -209,6 +209,12 @@ surface_analysis:
abcd_prefreesurfer_prep:
run: Off

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
Expand Down Expand Up @@ -580,12 +586,6 @@ registration_workflows:
# It is for monkey pipeline specifically.
FNIRT_T1w_template:

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

# Configuration file to be used by FSL to set FNIRT parameters.
# It is not necessary to change this path unless you intend to use custom FNIRT parameters or a non-standard template.
fnirt_config: T1_2_MNI152_2mm
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12 changes: 6 additions & 6 deletions CPAC/resources/configs/pipeline_config_default.yml
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Expand Up @@ -197,6 +197,12 @@ surface_analysis:
abcd_prefreesurfer_prep:
run: Off

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

# Will run Freesurfer for surface-based analysis. Will output traditional Freesurfer derivatives.
# If you wish to employ Freesurfer outputs for brain masking or tissue segmentation in the voxel-based pipeline,
# select those 'Freesurfer-' labeled options further below in anatomical_preproc.
Expand Down Expand Up @@ -738,12 +744,6 @@ registration_workflows:
# It is not necessary to change this path unless you intend to use a different template.
identity_matrix: $FSLDIR/etc/flirtsch/ident.mat

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2: $FSLDIR/data/standard/MNI152_T1_2mm_brain_mask_dil.nii.gz

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2: $FSLDIR/data/standard/MNI152_T1_2mm.nii.gz

overwrite_transform:

run: Off
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6 changes: 0 additions & 6 deletions CPAC/resources/configs/pipeline_config_fmriprep-options.yml
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Expand Up @@ -151,12 +151,6 @@ registration_workflows:
registration:
FSL-FNIRT:

# Reference mask with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
ref_mask_res-2:

# Template with 2mm resolution to be used during FNIRT-based brain extraction in ABCD-options pipeline.
T1w_template_res-2:

# Reference mask for FSL registration.
ref_mask:

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4 changes: 2 additions & 2 deletions CPAC/resources/cpac_templates.csv
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Expand Up @@ -31,8 +31,8 @@ T1w-template-symmetric,"voxel_mirrored_homotopic_connectivity, symmetric_registr
T1w-template-symmetric-deriv,"voxel_mirrored_homotopic_connectivity, symmetric_registration, T1w_template_symmetric_funcreg","Symmetric version of the T1w-based whole-head template, resampled to the desired functional derivative resolution","registration_workflows, functional_registration, func_registration_to_template, output_resolution, func_derivative_outputs"
T1w-template-symmetric-for-resample,"voxel_mirrored_homotopic_connectivity, symmetric_registration, T1w_template_symmetric_for_resample",,
template-ref-mask,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask",,"registration_workflows, anatomical_registration, resolution_for_anat"
template-ref-mask-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, ref_mask_res-2",,
T1w-template-res-2,"registration_workflows, anatomical_registration, registration, FSL-FNIRT, T1w_template_res-2",,
template-ref-mask-res-2,"surface_analysis, abcd_prefreesurfer_prep, ref_mask_res-2",,
T1w-template-res-2,"surface_analysis, abcd_prefreesurfer_prep, T1w_template_res-2",,
template-specification-file,"network_centrality, template_specification_file",Binary ROI mask for network centrality calculations,
unet-model,"anatomical_preproc, brain_extraction, UNet, unet_model",,
WM-path,"segmentation, tissue_segmentation, FSL-FAST, use_priors, WM_path",Template-space WM tissue prior,
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