diff --git a/modules/nf-scil/registration/synthregistration/main.nf b/modules/nf-scil/registration/synthregistration/main.nf index da027e7aa..5ceb177e5 100644 --- a/modules/nf-scil/registration/synthregistration/main.nf +++ b/modules/nf-scil/registration/synthregistration/main.nf @@ -11,7 +11,7 @@ process REGISTRATION_SYNTHREGISTRATION { output: tuple val(meta), path("*__output_warped.nii.gz"), emit: warped_image - tuple val(meta), path("*__deform_warp.m3z"), emit: deform_transform + tuple val(meta), path("*__deform_warp.nii.gz"), emit: deform_transform tuple val (meta), path("*__init_warp.lta"), emit: init_transform path "versions.yml" , emit: versions @@ -31,16 +31,13 @@ process REGISTRATION_SYNTHREGISTRATION { def extent = task.ext.extent ? "-e " + task.ext.extent : "" def weight = task.ext.weight ? "-w " + task.ext.weight : "" - //For arguments definition, mri_warp_convert -h - def out_format = task.ext.out_format ? "--out" + task.ext.out_format : "--outlps" - """ export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1 export OMP_NUM_THREADS=1 export OPENBLAS_NUM_THREADS=1 mri_synthmorph $init -g -t ${prefix}__init_warp.lta $moving $fixed - mri_synthmorph $warp -g -i ${prefix}__init_warp.lta -t ${prefix}__deform_warp.m3d -o ${prefix}__output_warped.nii.gz $moving $fixed + mri_synthmorph $warp -g -i ${prefix}__init_warp.lta -t ${prefix}__deform_warp.nii.gz -o ${prefix}__output_warped.nii.gz $moving $fixed cat <<-END_VERSIONS > versions.yml "${task.process}": diff --git a/modules/nf-scil/registration/synthregistration/meta.yml b/modules/nf-scil/registration/synthregistration/meta.yml index 2ec3d83f9..e4ba75452 100644 --- a/modules/nf-scil/registration/synthregistration/meta.yml +++ b/modules/nf-scil/registration/synthregistration/meta.yml @@ -7,8 +7,8 @@ keywords: - MRI tools: - "Freesurfer": - description: "Freesurfer Toolbox" - homepage: "https://surfer.nmr.mgh.harvard.edu/" + description: "Freesurfer Synthmorph" + homepage: "https://martinos.org/malte/synthmorph/" input: @@ -48,7 +48,7 @@ output: - deform_transform: type: file description: Deform transformation - pattern: "*.{m3z}" + pattern: "*.{nii,.nii.gz}" - warped_image: type: file diff --git a/tests/config/nextflow.config b/tests/config/nextflow.config index 9da264135..95f3737fc 100755 --- a/tests/config/nextflow.config +++ b/tests/config/nextflow.config @@ -5,8 +5,8 @@ params { } process { - cpus = 4 - memory = 5.GB + cpus = 16 + memory = 20.GB time = 2.h } diff --git a/tests/modules/nf-scil/registration/synthregistration/test.yml b/tests/modules/nf-scil/registration/synthregistration/test.yml index 49c0e31be..c99172969 100644 --- a/tests/modules/nf-scil/registration/synthregistration/test.yml +++ b/tests/modules/nf-scil/registration/synthregistration/test.yml @@ -1,11 +1,22 @@ - name: registration synthregistration test_registration_synthregistration command: nextflow run ./tests/modules/nf-scil/registration/synthregistration -entry test_registration_synthregistration -c ./tests/config/nextflow.config tags: - - "registration" - - "registration/synthregistration" + - registration + - registration/synthregistration files: - - path: "output/registration/test.bam" - md5sum: e667c7caad0bc4b7ac383fd023c654fc - - path: "output/registration/versions.yml" - md5sum: a01fe51bc4c6a3a6226fbf77b2c7cf3b - + - path: output/registration/test__deform_warp.nii.gz + md5sum: e0ed8084afa172668f50579f0585706c + - path: output/registration/test__init_warp.lta + md5sum: 4c5b29a64c8db1f87dd9ecf83a2d9878 + - path: output/registration/test__output_warped.nii.gz + md5sum: 2b0441e95fd48bc269833d05831cfd9e + - path: output/registration/versions.yml + - path: output/testdata/test_data/freesurfer/anat_image.nii.gz + md5sum: ba57c629e9dc29204215dceac36d65ae + - path: output/testdata/test_data/freesurfer/fa.nii.gz + md5sum: 0e76e9378500de64d66ba3d787a147ca + - path: output/testdata/test_data/freesurfer/license.txt + md5sum: 3db0fa4e1860b4774c7855980e406275 + - path: output/testdata/test_data/freesurfer/t1.nii.gz + md5sum: a6ade205420f594737ad67f9fb246f0f + - path: output/testdata/versions.yml