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Merge pull request #62 from scilus/revert-57-revert-25-fix-synthregis…
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[ENH] Update registration subworkflows and modules
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@arnaudbore
arnaudbore authored Dec 5, 2024
2 parents 9ed218f + c421af5 commit b0aa9b0
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Showing 13 changed files with 361 additions and 174 deletions.
36 changes: 20 additions & 16 deletions modules/nf-neuro/registration/convert/main.nf
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Original file line number Diff line number Diff line change
Expand Up @@ -6,11 +6,11 @@ process REGISTRATION_CONVERT {
containerOptions "--env FSLOUTPUTTYPE='NIFTI_GZ'"

input:
tuple val(meta), path(affine), path(deform), path(source), path(target), path(fs_license)
tuple val(meta), path(deform), path(affine), path(source), path(target), path(fs_license)

output:
tuple val(meta), path("*.{txt,lta,mat,dat}"), emit: affine_transform
tuple val(meta), path("*.{nii,nii.gz,mgz,m3z}"), emit: deform_transform
tuple val(meta), path("*out_deform_warp.{nii,nii.gz,mgz,m3z}") , emit: deform_transform
tuple val(meta), path("*out_affine_warp.{txt,lta,mat,dat}") , emit: affine_transform, optional: true
path "versions.yml" , emit: versions

when:
Expand Down Expand Up @@ -40,15 +40,20 @@ process REGISTRATION_CONVERT {
cp $fs_license \$FREESURFER_HOME/license.txt
declare -A affine_dictionnary=( ["--outlta"]="lta" \
["--outfsl"]="mat" \
["--outmni"]="xfm" \
["--outreg"]="dat" \
["--outniftyreg"]="txt" \
["--outitk"]="txt" \
["--outvox"]="txt" )
if [[ -f "$affine" ]];
then
declare -A affine_dictionnary=( ["--outlta"]="lta" \
["--outfsl"]="mat" \
["--outmni"]="xfm" \
["--outreg"]="dat" \
["--outniftyreg"]="txt" \
["--outitk"]="txt" \
["--outvox"]="txt" )
ext_affine=\${affine_dictionnary[${out_format_affine}]}
ext_affine=\${affine_dictionnary[${out_format_affine}]}
lta_convert ${invert} ${source_geometry_affine} ${target_geometry_affine} ${in_format_affine} ${out_format_affine} ${prefix}__out_affine_warp.\${ext_affine}
fi
declare -A deform_dictionnary=( ["--outm3z"]="m3z" \
["--outfsl"]="nii.gz" \
Expand All @@ -59,14 +64,13 @@ process REGISTRATION_CONVERT {
ext_deform=\${deform_dictionnary[${out_format_deform}]}
lta_convert ${invert} ${source_geometry_affine} ${target_geometry_affine} ${in_format_affine} ${out_format_affine} ${prefix}__affine_warp.\${ext_affine}
mri_warp_convert ${source_geometry_deform} ${downsample} ${in_format_deform} ${out_format_deform} ${prefix}__deform_warp.\${ext_deform}
mri_warp_convert ${source_geometry_deform} ${downsample} ${in_format_deform} ${out_format_deform} ${prefix}__out_deform_warp.\${ext_deform}
rm \$FREESURFER_HOME/license.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Freesurfer: 7.4.1
Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""

Expand All @@ -78,12 +82,12 @@ process REGISTRATION_CONVERT {
lta_convert -h
mri_warp_convert -h
touch ${prefix}__affine_transform.txt
touch ${prefix}__deform_transform.nii.gz
touch ${prefix}__affine_transform.txt
cat <<-END_VERSIONS > versions.yml
"${task.process}":
Freesurfer: 7.4.1
Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
END_VERSIONS
"""
}
20 changes: 10 additions & 10 deletions modules/nf-neuro/registration/convert/meta.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -19,16 +19,16 @@ input:
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
- affine:
type: file
description: Affine transform to convert. Default usage expects Freesurfer .lta format from mri_synthmorph
pattern: "*.{lta,txt,xfm,dat}"

- deform:
type: file
description: Deform transform to convert. Default usage expects Freesurfer .mgz format from mri_synthmorph
pattern: "*.{nii,nii.gz,mgz,m3z}"

- affine:
type: file
description: Affine transform to convert. Default usage expects Freesurfer .lta format from mri_synthmorph
pattern: "*.{lta,txt,xfm,dat}"

- source:
type: file
description: Moving Nifti volume used for registration. Defines source image geometry
Expand All @@ -51,16 +51,16 @@ output:
Groovy Map containing sample information
e.g. `[ id:'test', single_end:false ]`
- affine_transform:
type: file
description: Affine transform. Default usage outputs ANTs (ITK) format .txt
pattern: "*.{txt,lta,mat,dat}"

- deform_transform:
type: file
description: Deform transform. Default usage outputs ANTs (ITK) format .nii.gz
pattern: "*.{nii,nii.gz,mgz,m3z}"

- affine_transform:
type: file
description: Affine transform. Default usage outputs ANTs (ITK) format .txt
pattern: "*.{txt,lta,mat,dat}"

- versions:
type: file
description: File containing software versions
Expand Down
66 changes: 57 additions & 9 deletions modules/nf-neuro/registration/convert/tests/main.nf.test
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Original file line number Diff line number Diff line change
Expand Up @@ -41,8 +41,8 @@ nextflow_process {
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fs_affine.lta"),
file("\${test_data_directory}/fs_deform.nii.gz"),
[]
]
}
ch_reslice = ch_split_test_data.reslice.map{
Expand Down Expand Up @@ -73,6 +73,54 @@ nextflow_process {
}
}

test("registration - convert - affine") {

config "./nextflow_default.config"

when {
process {
"""
ch_split_test_data = LOAD_DATA.out.test_data_directory
.branch{
freesurfer: it.simpleName == "freesurfer"
reslice: it.simpleName == "freesurfer_reslice"
transforms: it.simpleName == "freesurfer_transforms"
}
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fs_deform.nii.gz"),
file("\${test_data_directory}/fs_affine.lta")
]
}
ch_reslice = ch_split_test_data.reslice.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/t1_reslice.nii.gz"),
file("\${test_data_directory}/fa_reslice.nii.gz")
]
}
ch_freesurfer = ch_split_test_data.freesurfer.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/license.txt")
]
}
input[0] = ch_transforms
.join(ch_reslice)
.join(ch_freesurfer)
"""
}
}

then {
assertAll(
{ assert process.success },
{ assert snapshot(process.out).match() }
)
}
}

test("registration - convert - fsants") {

config "./nextflow_fsants.config"
Expand All @@ -89,8 +137,8 @@ nextflow_process {
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fs_affine.lta"),
file("\${test_data_directory}/fs_deform.nii.gz")
file("\${test_data_directory}/fs_deform.nii.gz"),
file("\${test_data_directory}/fs_affine.lta")
]
}
ch_reslice = ch_split_test_data.reslice.map{
Expand Down Expand Up @@ -137,8 +185,8 @@ nextflow_process {
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fsl_affine.mat"),
file("\${test_data_directory}/fsl_deform.nii.gz")
file("\${test_data_directory}/fsl_deform.nii.gz"),
file("\${test_data_directory}/fsl_affine.mat")
]
}
ch_reslice = ch_split_test_data.reslice.map{
Expand Down Expand Up @@ -189,8 +237,8 @@ nextflow_process {
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/fsl_affine.mat"),
file("\${test_data_directory}/fsl_deform.nii.gz")
file("\${test_data_directory}/fsl_deform.nii.gz"),
file("\${test_data_directory}/fsl_affine.mat")
]
}
ch_reslice = ch_split_test_data.reslice.map{
Expand Down Expand Up @@ -237,8 +285,8 @@ nextflow_process {
ch_transforms = ch_split_test_data.transforms.map{
test_data_directory -> [
[ id:'test' ],
file("\${test_data_directory}/ants_affine.txt"),
file("\${test_data_directory}/ants_deform.nii.gz")
file("\${test_data_directory}/ants_deform.nii.gz"),
file("\${test_data_directory}/ants_affine.txt")
]
}
ch_reslice = ch_split_test_data.reslice.map{
Expand Down
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