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[ENH] Update registration subworkflows and modules #25

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[ENH] Update registration subworkflows and modules #25

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ec12dca
change transform output to fit other registration modules tuple(meta,…
anroy1 Oct 24, 2024
762eb0f
run tests
anroy1 Oct 25, 2024
306eb86
change inputs order to harmonize with other registration modules
anroy1 Oct 25, 2024
89ae309
add python path for tools and change output structure
anroy1 Oct 29, 2024
7794700
modify convert module
anroy1 Oct 29, 2024
df9ad98
add synthregistration optionnality to registration subworkflow
anroy1 Oct 29, 2024
e633175
add synthmorph option to registration subworkflow
anroy1 Oct 29, 2024
b4a94bd
update test
anroy1 Oct 29, 2024
4cd22c1
add versions to synthregistration tests
anroy1 Oct 29, 2024
f4111ea
fix Arnaud's comments
anroy1 Oct 30, 2024
659a2f0
fix and run tests
anroy1 Oct 31, 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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