[ENH] Fix registration + use mask apply in tractoflow #369
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -43,6 +43,15 @@ args: | |
| type: integer | ||
| description: Random seed for ANTs registration. Setting a fixed seed can help with reproducibility of results. | ||
| default: 1234 | ||
| - masking_strategy: | ||
| type: string | ||
| choices: | ||
| - none | ||
| - apriori | ||
| - internal | ||
| - both | ||
| description: Masking strategy to use for registration. Options are 'none', 'apriori', 'internal' or 'both'. | ||
| default: "none" | ||
| input: | ||
| - - meta: | ||
| type: map | ||
|
|
@@ -70,6 +79,20 @@ input: | |
| mandatory: true | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_4001 # NIFTI format | ||
| - fixed_mask: | ||
| type: file | ||
| description: Fixed image mask | ||
| pattern: "*.{nii,nii.gz}" | ||
| mandatory: false | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_4001 # NIFTI format | ||
| - moving_mask: | ||
| type: file | ||
| description: Moving image mask | ||
| pattern: "*.{nii,nii.gz}" | ||
| mandatory: false | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_4001 # NIFTI format | ||
| output: | ||
| anat_warped: | ||
| - - meta: | ||
|
|
@@ -83,6 +106,18 @@ output: | |
| pattern: "*_warped.nii.gz" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_4001 # NIFTI format | ||
| fixed_warped: | ||
| - - meta: | ||
| type: map | ||
| description: | | ||
| Groovy Map containing sample information | ||
| e.g. `[ id:'test', single_end:false ]` | ||
| - "*_warped_reference.nii.gz": | ||
| type: file | ||
| description: B0 warped to T1 space | ||
| pattern: "*_warped_reference.nii.gz" | ||
| ontologies: | ||
| - edam: http://edamontology.org/format_4001 # NIFTI format | ||
| forward_affine: | ||
| - - meta: | ||
| type: map | ||
|
|
||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -56,6 +56,59 @@ nextflow_process { | |
| input[0] = ch_b0 | ||
| .join(ch_t1w) | ||
| .join(ch_fa) | ||
| .map{ meta, fixed, moving, fixed_metric -> [meta, fixed, moving, fixed_metric, [], []] } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
| then { | ||
| assertAll( | ||
| { assert process.success }, | ||
| { assert snapshot(process.out).match() } | ||
| ) | ||
| } | ||
| } | ||
|
|
||
| test("registration - anattodwi - fixed mask") { | ||
| config "./nextflow.config" | ||
| when { | ||
| process { | ||
| """ | ||
| ch_split_test_data = LOAD_DATA.out.test_data_directory | ||
| .branch{ | ||
| t1w: it.simpleName == "T1w" | ||
| b0: it.simpleName == "b0" | ||
| dti: it.simpleName == "dti" | ||
| } | ||
| ch_t1w = ch_split_test_data.t1w.map{ | ||
| test_data_directory -> [ | ||
| [ id:'test', single_end:false ], | ||
| file("\${test_data_directory}/T1w.nii.gz") | ||
| ] | ||
| } | ||
| ch_b0 = ch_split_test_data.b0.map{ | ||
| test_data_directory -> [ | ||
| [ id:'test', single_end:false ], | ||
| file("\${test_data_directory}/b0.nii.gz") | ||
| ] | ||
| } | ||
| ch_fa = ch_split_test_data.dti.map{ | ||
| test_data_directory -> [ | ||
| [ id:'test', single_end:false ], | ||
| file("\${test_data_directory}/fa.nii.gz") | ||
| ] | ||
| } | ||
| ch_fixed_mask = ch_split_test_data.t1w.map{ | ||
| test_data_directory -> [ | ||
| [ id:'test', single_end:false ], | ||
| file("\${test_data_directory}/T1w_mask.nii.gz") | ||
| ] | ||
| } | ||
| input[0] = ch_b0 | ||
| .join(ch_t1w) | ||
| .join(ch_fa) | ||
| .join(ch_fixed_mask) | ||
| .map{ meta, fixed, moving, fixed_metric, fixed_mask -> [meta, fixed, moving, fixed_metric, fixed_mask, []] } | ||
| """ | ||
| } | ||
| } | ||
|
|
@@ -101,6 +154,7 @@ nextflow_process { | |
| input[0] = ch_b0 | ||
| .join(ch_t1w) | ||
| .join(ch_fa) | ||
| .map{ meta, fixed, moving, fixed_metric -> [meta, fixed, moving, fixed_metric, [], []] } | ||
| """ | ||
| } | ||
| } | ||
|
|
||
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Worth calling out in the PR description / release notes: this changes the input cardinality from 4 to 6, so every external caller of
REGISTRATION_ANATTODWImust add[], []. It fails loudly rather than silently, so it is much less dangerous than themasking_strategydefault change — but it is still a breaking API change for anyone who has installed this module.