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[ENH] Update registration subworkflows and modules #62

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Dec 5, 2024
Merged

[ENH] Update registration subworkflows and modules #62

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964d3f4
Revert "Revert "[ENH] Update registration subworkflows and modules""
AlexVCaron Dec 2, 2024
7326196
remove condition on channel, comment and improve readability
AlexVCaron Dec 3, 2024
a27bd11
fix test, update snap
AlexVCaron Dec 4, 2024
bf99204
Merge branch 'main' into revert-57-revert-25-fix-synthregistration
AlexVCaron Dec 4, 2024
c421af5
fix version for synthreg module
AlexVCaron Dec 5, 2024
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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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