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[Improvement] add synthbet option to preproc_t1 #169

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[Improvement] add synthbet option to preproc_t1 #169

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8c0355c
[WIP] Initial module commit
anroy1 Jul 3, 2024
5afe64d
[WIP] Add contitionnality for ants vs synth input
anroy1 Jul 4, 2024
4fca884
[WIP] fix testing
anroy1 Jul 26, 2024
d57e827
run tests and lint
anroy1 Jul 30, 2024
9eb5213
Manage synth conditionnality through params instead of input
anroy1 Aug 27, 2024
61320e8
Change val name synth for surgery
anroy1 Aug 31, 2024
f77ce5b
Push tests snap
anroy1 Aug 31, 2024
dc68c63
Use niftiMD5SUM
anroy1 Sep 8, 2024
d684221
Switch param name back to run_synth
anroy1 Sep 17, 2024
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50 changes: 36 additions & 14 deletions subworkflows/nf-scil/preproc_t1/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -3,18 +3,22 @@ include { DENOISING_NLMEANS } from '../../../modules/nf-scil/denoising/nlmeans/m
include { PREPROC_N4 } from '../../../modules/nf-scil/preproc/n4/main'
include { IMAGE_RESAMPLE } from '../../../modules/nf-scil/image/resample/main'
include { BETCROP_ANTSBET } from '../../../modules/nf-scil/betcrop/antsbet/main'
include { BETCROP_SYNTHBET} from '../../../modules/nf-scil/betcrop/synthbet/main'
include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_T1 } from '../../../modules/nf-scil/betcrop/cropvolume/main'
include { BETCROP_CROPVOLUME as BETCROP_CROPVOLUME_MASK } from '../../../modules/nf-scil/betcrop/cropvolume/main'

params.run_synthbet = params.run_synthbet ?: false

workflow PREPROC_T1 {

take:
ch_image // channel: [ val(meta), [ image ] ]
ch_template // channel: [ val(meta), [ template ] ]
ch_probability_map // channel: [ val(meta), [ probability_map ] ]
ch_template // channel: [ val(meta), [ template ] ] , optional
ch_probability_map // channel: [ val(meta), [ probability_map ] ] , optional
ch_mask_nlmeans // channel: [ val(meta), [ mask ] ] , optional
ch_ref_n4 // channel: [ val(meta), [ ref, ref_mask ] ] , optional
ch_ref_resample // channel: [ val(meta), [ ref ] ] , optional
ch_weights // channel: [ val(meta), [ weights ] ] , optional

main:

Expand All @@ -36,28 +40,46 @@ workflow PREPROC_T1 {
ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())

// ** Brain extraction ** //
ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
BETCROP_ANTSBET ( ch_bet )
ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
if ( params.run_synthbet) {
ch_bet = IMAGE_RESAMPLE.out.image.join(ch_weights)
BETCROP_SYNTHBET ( ch_bet )
ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())

// ** Setting BET output ** //
image_bet = BETCROP_SYNTHBET.out.bet_image
mask_bet = BETCROP_SYNTHBET.out.brain_mask
}

else {
ch_template = ch_template.ifEmpty(Channel.error('Template is required for ANTS registration'))
ch_probability_map = ch_probability_map.ifEmpty(Channel.error('Probability map is required for ANTS registration'))
ch_bet = IMAGE_RESAMPLE.out.image.join(ch_template).join(ch_probability_map)
BETCROP_ANTSBET ( ch_bet )
ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())

// ** Setting BET output ** //
image_bet = BETCROP_ANTSBET.out.t1
mask_bet = BETCROP_ANTSBET.out.mask
}

// ** crop image ** //
ch_crop = BETCROP_ANTSBET.out.t1.map{it + [[]]}
ch_crop = image_bet.map{it + [[]]}
BETCROP_CROPVOLUME_T1 ( ch_crop )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_T1.out.versions.first())

// ** crop mask ** //
ch_crop_mask = BETCROP_ANTSBET.out.mask.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
ch_crop_mask = mask_bet.join(BETCROP_CROPVOLUME_T1.out.bounding_box)
BETCROP_CROPVOLUME_MASK ( ch_crop_mask )
ch_versions = ch_versions.mix(BETCROP_CROPVOLUME_MASK.out.versions.first())

emit:
image_nlmeans = DENOISING_NLMEANS.out.image // channel: [ val(meta), [ image ] ]
image_N4 = PREPROC_N4.out.image // channel: [ val(meta), [ image ] ]
image_resample = IMAGE_RESAMPLE.out.image // channel: [ val(meta), [ image ] ]
image_bet = BETCROP_ANTSBET.out.t1 // channel: [ val(meta), [ t1 ] ]
mask_bet = BETCROP_ANTSBET.out.mask // channel: [ val(meta), [ mask ] ]
image_nlmeans = DENOISING_NLMEANS.out.image // channel: [ val(meta), [ image ] ]
image_N4 = PREPROC_N4.out.image // channel: [ val(meta), [ image ] ]
image_resample = IMAGE_RESAMPLE.out.image // channel: [ val(meta), [ image ] ]
image_bet = image_bet // channel: [ val(meta), [ t1 ] ]
mask_bet = mask_bet // channel: [ val(meta), [ mask ] ]
crop_box = BETCROP_CROPVOLUME_T1.out.bounding_box // channel: [ val(meta), [ bounding_box ] ]
mask_final = BETCROP_CROPVOLUME_MASK.out.image // channel: [ val(meta), [ mask ] ]
mask_final = BETCROP_CROPVOLUME_MASK.out.image // channel: [ val(meta), [ image ] ]
t1_final = BETCROP_CROPVOLUME_T1.out.image // channel: [ val(meta), [ image ] ]
versions = ch_versions // channel: [ versions.yml ]
versions = ch_versions // channel: [ versions.yml ]
}
14 changes: 13 additions & 1 deletion subworkflows/nf-scil/preproc_t1/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -21,7 +21,7 @@ description: |
Resamples the T1 to an isotropic spatial resolution. The default is 1mm, a standard in humans which
usually facilitate registration with corrected DWI images.
This spatial resolution is modifiable in the configuration file.
Brain Extraction (bet, ANTs).
Brain Extraction (bet, ANTs, freesurfer).
Isolates the brain tissue voxels from the remaining image. Also creates a binary brain mask.
This brain extraction is required for the T1 to DWI Registration.
Cropping (scil).
Expand All @@ -42,6 +42,7 @@ components:
- preproc/n4
- image/resample
- betcrop/antsbet
- betcrop/synthbet
- betcrop/cropvolume

input:
Expand Down Expand Up @@ -81,6 +82,17 @@ input:
The input channel containing the reference for the resampling. Optional
Structure: [ val(meta), path(ref) ]
pattern: "*.{nii,nii.gz}"
- ch_weights:
type: file
description: |
The input channel containing an alternative model weights for synthbet. Optional
Structure: [ val(meta), path (weights)]
pattern: "*.pt"
- val_synth:
type: boolean
description: |
Boolean input specifying which BET method is employed. Optional: defaults at false (ANTs)
pattern: "true"
output:
- image_nlmeans:
type: file
Expand Down
104 changes: 102 additions & 2 deletions subworkflows/nf-scil/preproc_t1/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -12,6 +12,7 @@ nextflow_workflow {
tag "preproc/n4"
tag "image/resample"
tag "betcrop/antsbet"
tag "betcrop/synthbet"
tag "betcrop/cropvolume"

tag "load_test_data"
Expand Down Expand Up @@ -69,14 +70,29 @@ nextflow_workflow {
[ id:'test', single_end:false ],
[]
]}
input[6] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
"""
}
}

then {
assertAll(
{ assert workflow.success},
{ assert snapshot(workflow.out).match()}
{ assert snapshot(
niftiMD5SUM(workflow.out.image_nlmeans.get(0).get(1)),
niftiMD5SUM(workflow.out.image_N4.get(0).get(1)),
niftiMD5SUM(workflow.out.image_resample.get(0).get(1)),
niftiMD5SUM(workflow.out.image_bet.get(0).get(1)),
niftiMD5SUM(workflow.out.mask_bet.get(0).get(1)),
file(workflow.out.crop_box.get(0).get(1)),
niftiMD5SUM(workflow.out.mask_final.get(0).get(1)),
niftiMD5SUM(workflow.out.t1_final.get(0).get(1)),
workflow.out.versions
).match()}
)
}
}
Expand Down Expand Up @@ -123,14 +139,98 @@ nextflow_workflow {
[ id:'test', single_end:false ],
file("\${test_data_directory}/t1_unaligned.nii.gz")
]}
input[6] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
"""
}
}

then {
assertAll(
{ assert workflow.success},
{ assert snapshot(
niftiMD5SUM(workflow.out.image_nlmeans.get(0).get(1)),
niftiMD5SUM(workflow.out.image_N4.get(0).get(1)),
niftiMD5SUM(workflow.out.image_resample.get(0).get(1)),
niftiMD5SUM(workflow.out.image_bet.get(0).get(1)),
niftiMD5SUM(workflow.out.mask_bet.get(0).get(1)),
workflow.out.crop_box,
niftiMD5SUM(workflow.out.mask_final.get(0).get(1)),
niftiMD5SUM(workflow.out.t1_final.get(0).get(1)),
workflow.out.versions
).match()}
)
}
}

test("preproc_t1_synthbet") {
config "./nextflow_synthbet.config"

when {
workflow {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
antsbet: it.simpleName == "antsbet"
others: it.simpleName == "others"
}
input[0] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
file("\${test_data_directory}/t1_unaligned.nii.gz")
]}
input[1] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
input[2] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
input[3] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
input[4] = ch_split_test_data.others.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[],
[]
]}
input[5] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
input[6] = ch_split_test_data.antsbet.map{
test_data_directory -> [
[ id:'test', single_end:false ],
[]
]}
"""
}
}

then {
assertAll(
{ assert workflow.success},
{ assert snapshot(workflow.out).match()}
{ assert snapshot(
niftiMD5SUM(workflow.out.image_nlmeans.get(0).get(1)),
niftiMD5SUM(workflow.out.image_N4.get(0).get(1)),
niftiMD5SUM(workflow.out.image_resample.get(0).get(1)),
niftiMD5SUM(workflow.out.image_bet.get(0).get(1)),
niftiMD5SUM(workflow.out.mask_bet.get(0).get(1)),
workflow.out.crop_box,
niftiMD5SUM(workflow.out.mask_final.get(0).get(1)),
niftiMD5SUM(workflow.out.t1_final.get(0).get(1)),
workflow.out.versions
).match()}
)
}
}
Expand Down
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