diff --git a/modules/nf-neuro/registration/cobralab_ants/environment.yml b/modules/nf-neuro/registration/cobralab_ants/environment.yml
new file mode 100644
index 00000000..2c00919a
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: registration_ants
diff --git a/modules/nf-neuro/registration/cobralab_ants/main.nf b/modules/nf-neuro/registration/cobralab_ants/main.nf
new file mode 100644
index 00000000..46bb9ef1
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/main.nf
@@ -0,0 +1,188 @@
+
+process REGISTRATION_COBRALABANTS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "scilus/scilus:2.2.1"
+
+    input:
+        tuple val(meta), path(fixed_image), path(moving_image), path(mask)
+
+    output:
+        tuple val(meta), path("*_warped.nii.gz")                           , emit: image_warped
+        tuple val(meta), path("*_forward1_affine.mat")                     , emit: forward_affine, optional: true
+        tuple val(meta), path("*_forward0_warp.nii.gz")                    , emit: forward_warp, optional: true
+        tuple val(meta), path("*_backward1_warp.nii.gz")                   , emit: backward_warp, optional: true
+        tuple val(meta), path("*_backward0_affine.mat")                    , emit: backward_affine, optional: true
+        tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2')    , emit: forward_image_transform
+        tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: backward_image_transform
+        tuple val(meta), path("*_backward*.{nii.gz,mat}", arity: '1..2')   , emit: forward_tractogram_transform
+        tuple val(meta), path("*_forward*.{nii.gz,mat}", arity: '1..2')    , emit: backward_tractogram_transform
+        tuple val(meta), path("*_registration_ants_mqc.gif")               , emit: mqc, optional: true
+        path "versions.yml"                                                , emit: versions
+
+    when:
+        task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix_qc = task.ext.suffix_qc ?: ""
+    def run_qc = task.ext.run_qc as Boolean || false
+
+    if ( mask ) args += " --fixed-mask $mask"
+    // if ( moving_mask ) args += " --moving-mask $moving_mask"
+    if ( task.ext.initial_transform ) args += " --initial-transform $task.ext.initial_transform"
+    if ( task.ext.float ) args += " --float"
+    if ( task.ext.histogram_matching ) args += " --histogram-matching"
+    if ( task.ext.rough ) args += " --rough"
+    if ( task.ext.fast ) args += " --fast"
+    if ( task.ext.mask_extract ) args += " --mask-extract"
+    if ( task.ext.keep_mask_after_extract ) args += " --keep-mask-after-extract"
+    if ( task.ext.resampled_linear_output ) args += " --resampled-linear-output $task.ext.resampled_linear_output"
+    if ( task.ext.linear_type ) args += " --linear-type $task.ext.linear_type"
+    if ( task.ext.close ) args += " --close"
+    if ( task.ext.convergence != '1e-6' ) args += " --convergence $task.ext.convergence"
+    if ( task.ext.skip_linear ) args += " --skip-linear"
+    if ( task.ext.linear_metric != 'Mattes' ) args += " --linear-metric $task.ext.linear_metric"
+    if ( task.ext.linear_shrink_factors ) args += " --linear-shrink-factors $task.ext.linear_shrink_factors"
+    if ( task.ext.linear_smoothing_sigmas ) args += " --linear-smoothing-sigmas $task.ext.linear_smoothing_sigmas"
+    if ( task.ext.linear_convergence ) args += " --linear-convergence $task.ext.linear_convergence"
+    if ( task.ext.final_iterations_linear != '50' ) args += " --final-iterations-linear $task.ext.final_iterations_linear"
+    if ( task.ext.kmeans_transformed_linear ) args += " --kmeans-transformed-linear"
+    if ( task.ext.skip_nonlinear ) args += " --skip-nonlinear"
+    if ( task.ext.syn_control != '0.4,4,0' ) args += " --syn-control $task.ext.syn_control"
+    if ( task.ext.syn_metric != 'CC[4]' ) args += " --syn-metric $task.ext.syn_metric"
+    if ( task.ext.syn_shrink_factors ) args += " --syn-shrink-factors $task.ext.syn_shrink_factors"
+    if ( task.ext.syn_smoothing_sigmas ) args += " --syn-smoothing-sigmas $task.ext.syn_smoothing_sigmas"
+    if ( task.ext.syn_convergence ) args += " --syn-convergence $task.ext.syn_convergence"
+    if ( task.ext.final_iterations_nonlinear != '20' ) args += " --final-iterations-nonlinear $task.ext.final_iterations_nonlinear"
+    if ( task.ext.winsorize_image_intensities ) args += " --winsorize-image-intensities $task.ext.winsorize_image_intensities"
+    if ( task.ext.clobber ) args += " --clobber"
+    if ( task.ext.verbose == false ) args += " --no-verbose"
+    if ( task.ext.debug ) args += " --debug"
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    moving_id=\$(basename $moving_image .nii.gz)
+    moving_id=\${moving_id#${meta.id}_*}
+
+    antsRegistration_affine_SyN.sh $args --resampled-output ${prefix}_\${moving_id}_warped.nii.gz $moving_image $fixed_image output
+
+    if [ ${task.ext.skip_linear} == false ]; then
+        mv output0GenericAffine.mat ${prefix}_forward1_affine.mat
+    fi
+
+    if [ ${task.ext.skip_nonlinear} == false ]; then
+        mv output1InverseWarp.nii.gz ${prefix}_backward1_warp.nii.gz
+        mv output1Warp.nii.gz ${prefix}_forward0_warp.nii.gz
+    fi
+
+    antsApplyTransforms -d 3 -t [${prefix}_forward1_affine.mat,1] \
+        -o Linear[${prefix}_backward0_affine.mat]
+
+    ### ** QC ** ###
+    if $run_qc; then
+        mv $fixed_image fixed_image.nii.gz
+        extract_dim=\$(mrinfo fixed_image.nii.gz -size)
+        read sagittal_dim coronal_dim axial_dim <<< "\${extract_dim}"
+
+        # Get the middle slice
+        coronal_dim=\$((\$coronal_dim / 2))
+        axial_dim=\$((\$axial_dim / 2))
+        sagittal_dim=\$((\$sagittal_dim / 2))
+
+        # Get fixed ID, moving ID already computed
+        fixed_id=\$(basename $fixed_image .nii.gz)
+        fixed_id=\${fixed_id#${meta.id}_*}
+
+        # Set viz params.
+        viz_params="--display_slice_number --display_lr --size 256 256"
+        # Iterate over images.
+        for image in fixed_image warped; do
+            mrconvert *\${image}.nii.gz *\${image}_viz.nii.gz -stride -1,2,3
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_coronal.png \
+                --slices \$coronal_dim --axis coronal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_sagittal.png \
+                --slices \$sagittal_dim --axis sagittal \$viz_params
+            scil_viz_volume_screenshot *\${image}_viz.nii.gz \${image}_axial.png \
+                --slices \$axial_dim --axis axial \$viz_params
+
+            if [ \$image != fixed_image ]; then
+                title="Warped \${moving_id^^}"
+            else
+                title="Reference \${fixed_id^^}"
+            fi
+
+            convert +append \${image}_coronal*.png \${image}_axial*.png \
+                \${image}_sagittal*.png \${image}_mosaic.png
+            convert -annotate +20+230 "\${title}" -fill white -pointsize 30 \
+                \${image}_mosaic.png \${image}_mosaic.png
+
+            # Clean up.
+            rm \${image}_coronal*.png \${image}_sagittal*.png \${image}_axial*.png
+        done
+
+        # Create GIF.
+        convert -delay 10 -loop 0 -morph 10 \
+            warped_mosaic.png fixed_image_mosaic.png warped_mosaic.png \
+            ${prefix}_${suffix_qc}_registration_ants_mqc.gif
+
+        # Clean up.
+        rm *_mosaic.png
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
+        imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
+        mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix_qc = task.ext.suffix_qc ?: ""
+    def run_qc = task.ext.run_qc as Boolean || false
+
+    """
+    set +e
+    function handle_code () {
+        local code=\$?
+        ignore=( 1 )
+        [[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
+    }
+
+    # Local trap to ignore awaited non-zero exit codes
+    {
+        trap 'handle_code' ERR
+        antsRegistrationSyNQuick.sh -h
+    }
+
+    antsApplyTransforms -h
+    convert -help .
+    scil_viz_volume_screenshot -h
+
+    touch ${prefix}_t1_warped.nii.gz
+    touch ${prefix}_forward1_affine.mat
+    touch ${prefix}_forward0_warp.nii.gz
+    touch ${prefix}_backward1_warp.nii.gz
+    touch ${prefix}_backward0_affine.mat
+
+    if $run_qc; then
+        touch ${prefix}_${suffix_qc}_registration_ants_mqc.gif
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*: v?([0-9.a-zA-Z-]+).*/\\1/')
+        imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
+        mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/registration/cobralab_ants/meta.yml b/modules/nf-neuro/registration/cobralab_ants/meta.yml
new file mode 100644
index 00000000..4245c6ee
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/meta.yml
@@ -0,0 +1,354 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-neuro/modules/main/modules/meta-schema.json
+name: "registration_ants"
+description: |
+  Image registration with antsRegistration_affine_SyN.sh from CoBrALab with automatic optimal pyramid generation.
+
+  Defaults: 3D images and multi-stage registration (rigid + similarity + affine + deformable)
+
+  Main features:
+  (1) Supports multiple transformation types (see `transform` argument).
+  (2) Supports initial transformations (see `initial_transform` argument).
+  (3) Automatic creation of backward (inverse) transformations matrices.
+  (4) Curated combined output transformations for REGISTRATION_ANTSAPPLYTRANSFORMS and REGISTRATION_TRANSFORMTRACTOGRAM
+      processes : `forward_image_transform`, `forward_tractogram_transform`, and their `backward` versions.
+  (5) Quality control (QC) image generation for MultiQC reports.
+keywords:
+  - nifti
+  - registration
+  - antsRegistrationSyN
+  - antsRegistrationSyNQuick
+  - antsRegistration_affine_SyN
+tools:
+  - ANTs:
+      description: "Advanced Normalization Tools."
+      homepage: "https://github.com/ANTsX/ANTs"
+      documentation: "http://stnava.github.io/ANTsDoc/"
+      doi: "10.1038/s41598-021-87564-6"
+  - antsRegistration_affine_SyN.sh:
+      description: "Advanced Normalization Tools."
+      homepage: "https://github.com/CoBrALab/antsRegistration_affine_SyN"
+      documentation: "https://github.com/CoBrALab/antsRegistration_affine_SyN/blob/master/README.md"
+  - ImageMagick:
+      description: "ImageMagick is a software suite to create, edit, compose, or convert bitmap images."
+      homepage: "https://imagemagick.org/"
+      documentation: "https://imagemagick.org/script/command-line-processing.php"
+  - MRtrix3:
+      description: "MRtrix3 is a software package for processing diffusion MRI data."
+      homepage: "https://www.mrtrix3.org/"
+      documentation: "https://mrtrix.readthedocs.io/en/latest/"
+      doi: "10.1016/j.neuroimage.2019.116137"
+  - Scilpy:
+      description: "Scilpy is a Python library for processing diffusion MRI data."
+      homepage: "https://github.com/scilus/scilpy"
+      documentation: "https://scilpy.readthedocs.io/en/latest/"
+args:
+  - fast:
+      type: boolean
+      description: "Use Mattes for deformation registration stages"
+      default: false
+  - histogram_matching:
+      type: boolean
+      description: "Perform histogram matching between images before registration."
+      default: false
+  - initial_transform:
+      type: string
+      description: Algorithmic initialization by geometric center, intensities, or origin or nothing
+      default: "com-masks"
+      choices:
+        - com-masks
+        - com
+        - cov
+        - origin
+        - none
+  - run_qc:
+      type: boolean
+      description: "Run quality control (QC) to generate a MultiQC report."
+      default: false
+  - suffix_qc:
+      type: string
+      description: "Suffix for the QC image file."
+      default: ""
+  - mask_extract:
+      type: boolean
+      description: "Use masks to extract input images, only works with both images masked"
+      default: false
+  - keep_mask_after_extract:
+      type: boolean
+      description: "Keep using masks for metric after extraction"
+      default: false
+  - resampled_linear_output:
+      type: string
+      description: "Output resampled file(s) with only linear transform, repeat for resampling multispectral outputs"
+      default: ""
+  - linear_type:
+      type: string
+      description: "Type of linear transform"
+      default: "affine"
+      choices:
+        - "rigid"
+        - "lsq6"
+        - "similarity"
+        - "lsq9"
+        - "affine"
+        - "lsq12"
+  - close:
+      type: boolean
+      description: "Images are close in space and similarity, skip large scale pyramid search"
+      default: false
+  - weights:
+      type: string
+      description: "A single value, which disables weighting, or a comma separated list of weights, ordered primary pair, followed by multispectral pairs"
+      default: "1"
+  - convergence:
+      type: string
+      description: "Convergence stopping value for registration"
+      default: "1e-6"
+  - skip_linear:
+      type: boolean
+      description: "Skip the linear registration stages"
+      default: false
+  - linear_metric:
+      type: string
+      description: "Linear metric"
+      default: "Mattes"
+  - linear_shrink_factors:
+      type: string
+      description: "Override shrink factors for linear stage, provide to override automatic generation, must be provided with sigmas and convergence"
+      default: ""
+  - linear_smoothing_sigmas:
+      type: string
+      description: "Override smoothing sigmas for linear stage, provide to override automatic generation, must be provided with shrinks and convergence"
+      default: ""
+  - linear_convergence:
+      type: string
+      description: "Override convergence levels for linear stage, provide to override automatic generation, must be provided with shrinks and sigmas"
+      default: ""
+  - final_iterations_linear:
+      type: string
+      description: "Maximum iterations at finest scale for linear automatic generation"
+      default: "50"
+  - kmeans_transformed_linear:
+      type: boolean
+      description: "KMeans cluster image intensities for linear registration"
+      default: false
+  - skip_nonlinear:
+      type: boolean
+      description: "Skip the nonlinear stage"
+      default: false
+  - syn_control:
+      type: string
+      description: "Non-linear (SyN) gradient and regularization parameters, not checked for correctness"
+      default: "0.4,4,0"
+  - syn_metric:
+      type: string
+      description: "Non-linear (SyN) metric and radius or bins, choose Mattes[32] for faster registrations"
+      default: "CC[4]"
+  - syn_shrink_factors:
+      type: string
+      description: "Shrink factors for Non-linear (SyN) stage, provide to override automatic generation, must be provided with sigmas and convergence"
+      default: ""
+  - syn_smoothing_sigmas:
+      type: string
+      description: "Smoothing sigmas for Non-linear (SyN) stage, provide to override automatic generation, must be provided with shrinks and convergence"
+      default: ""
+  - syn_convergence:
+      type: string
+      description: "Convergence levels for Non-linear (SyN) stage, provide to override automatic generation, must be provided with shrinks and sigmas"
+      default: ""
+  - final_iterations_nonlinear:
+      type: string
+      description: "Maximum iterations at finest scale for non-linear automatic generation"
+      default: "20"
+  - winsorize_image_intensities:
+      type: string
+      description: "Winsorize data based on specified quantiles, comma separated lower,upper"
+      default: ""
+  - float:
+      type: boolean
+      description: "Calculate registration using float instead of double"
+      default: false
+  - clobber:
+      type: boolean
+      description: "Overwrite files that already exist"
+      default: false
+  - verbose:
+      type: boolean
+      description: "Run commands verbosely"
+      default: true
+  - debug:
+      type: boolean
+      description: "Show all internal commands and logic for debug"
+      default: false
+input:
+  - - meta:
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. `[ id:'test', single_end:false ]`
+    - fixed_image:
+        type: file
+        description: Fixed image(s) or source image(s) or reference image(s)
+        pattern: "*.{nii,nii.gz}"
+        mandatory: true
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
+    - moving_image:
+        type: file
+        description: Moving image(s) or target image(s)
+        pattern: "*.{nii,nii.gz}"
+        mandatory: true
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
+    - mask:
+        type: file
+        description: Mask for the fixed image
+        pattern: "*.{nii,nii.gz}"
+        mandatory: false
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
+    - moving_mask:
+        type: file
+        description: Mask for the moving image
+        pattern: "*.{nii,nii.gz}"
+        mandatory: false
+        ontologies:
+          - edam: http://edamontology.org/format_4001 # NIFTI format
+output:
+  image_warped:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_warped.nii.gz":
+          type: file
+          description: Nifti volume after registration.
+          pattern: "*_warped.nii.gz"
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  forward_affine:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_forward1_affine.mat":
+          type: file
+          description: Affine transformation from moving to fixed
+          pattern: "*_forward1_affine.mat"
+          mandatory: false
+          ontologies: []
+  forward_warp:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_forward0_warp.nii.gz":
+          type: file
+          description: Nifti volume containing warp field from moving to fixed
+          pattern: "*_forward0_warp.nii.gz"
+          mandatory: false
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  backward_warp:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_backward1_warp.nii.gz":
+          type: file
+          description: Nifti volume containing warp field from fixed to moving
+          pattern: "*_backward1_warp.nii.gz"
+          mandatory: false
+          ontologies:
+            - edam: http://edamontology.org/format_3989 # GZIP format
+  backward_affine:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_backward0_affine.mat":
+          type: file
+          description: Affine transformation from fixed to moving
+          pattern: "*_backward0_affine.mat"
+          mandatory: false
+          ontologies: []
+  forward_image_transform:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_forward*.{nii.gz,mat}":
+          type: list
+          description: |
+            Tuple, Transformation files to warp images in fixed space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_warp, forward_affine ] ].
+          pattern: "*_forward*.{nii.gz,mat}"
+          ontologies: []
+  backward_image_transform:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_backward*.{nii.gz,mat}":
+          type: list
+          description: |
+            Tuple, transformation files to warp images in moving space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].
+          pattern: "*_backward*.{nii.gz,mat}"
+          ontologies: []
+  forward_tractogram_transform:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_backward*.{nii.gz,mat}":
+          type: list
+          description: |
+            Tuple, transformation files to warp tractograms into fixed space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ backward_affine, backward_warp ] ].
+          pattern: "*_backward*.{nii.gz,mat}"
+          ontologies: []
+  backward_tractogram_transform:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_forward*.{nii.gz,mat}":
+          type: list
+          description: |
+            Tuple, transformation files to warp tractograms into moving space, in the correct order
+            for REGISTRATION_TRANSFORMTRACTOGRAM : [ meta, [ forward_affine, forward_warp ] ].
+          pattern: "*_forward*.{nii.gz,mat}"
+          ontologies: []
+  mqc:
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. `[ id:'test', single_end:false ]`
+      - "*_registration_ants_mqc.gif":
+          type: file
+          description: .gif file containing quality control image for the registration
+            process. Made for use in MultiQC report.
+          pattern: "*_registration_ants_mqc.gif"
+          mandatory: false
+          ontologies: []
+  versions:
+    - versions.yml:
+        type: file
+        description: File containing software versions
+        pattern: versions.yml
+        ontologies:
+          - edam: http://edamontology.org/format_3750 # YAML
+authors:
+  - "@ThoumyreStanislas"
+  - "@AlexVCaron"
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test b/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test
new file mode 100644
index 00000000..858003d4
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test
@@ -0,0 +1,195 @@
+nextflow_process {
+
+    name "Test Process REGISTRATION_COBRALABANTS"
+    script "../main.nf"
+    process "REGISTRATION_COBRALABANTS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfneuro"
+    tag "registration"
+    tag "registration/ants"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "T1w.zip", "others.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+    test("registration - ants - SyN") {
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        T1w: it.simpleName == "T1w"
+                        moving: it.simpleName == "others"
+                    }
+                ch_T1w = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_moving = ch_split_test_data.moving.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1.nii.gz")
+                    ]
+                }
+                ch_T1w_mask = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w_mask.nii.gz")
+                    ]
+                }
+                input[0] = ch_T1w
+                    .join(ch_moving)
+                    .join(ch_T1w_mask)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("registration - ants - SyN quick") {
+        config "./nextflow_quick.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        T1w: it.simpleName == "T1w"
+                        moving: it.simpleName == "others"
+                    }
+                ch_T1w = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_moving = ch_split_test_data.moving.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1.nii.gz")
+                    ]
+                }
+                ch_T1w_mask = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w_mask.nii.gz")
+                    ]
+                }
+                input[0] = ch_T1w
+                    .join(ch_moving)
+                    .join(ch_T1w_mask)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("registration - ants - no warps") {
+        config "./nextflow_no_warp.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        T1w: it.simpleName == "T1w"
+                        moving: it.simpleName == "others"
+                    }
+                ch_T1w = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_moving = ch_split_test_data.moving.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1.nii.gz")
+                    ]
+                }
+                ch_T1w_mask = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w_mask.nii.gz")
+                    ]
+                }
+                input[0] = ch_T1w
+                    .join(ch_moving)
+                    .join(ch_T1w_mask)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("registration - ants - stub") {
+        tag "stub"
+        options "-stub-run"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        T1w: it.simpleName == "T1w"
+                        moving: it.simpleName == "others"
+                    }
+                ch_T1w = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_moving = ch_split_test_data.moving.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1.nii.gz")
+                    ]
+                }
+                ch_T1w_mask = ch_split_test_data.T1w.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w_mask.nii.gz")
+                    ]
+                }
+                input[0] = ch_T1w
+                    .join(ch_moving)
+                    .join(ch_T1w_mask)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test.snap b/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test.snap
new file mode 100644
index 00000000..75d3eb00
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/main.nf.test.snap
@@ -0,0 +1,569 @@
+{
+    "registration - ants - stub": {
+        "content": [
+            [
+                "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T13:00:52.757761907"
+    },
+    "registration - ants - SyN quick": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,5534f8cb21fcc44f577d520e6083bb83"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                    ]
+                ],
+                "10": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe",
+                            "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30",
+                            "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                        ]
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30",
+                            "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                        ]
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe",
+                            "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                        ]
+                    ]
+                ],
+                "9": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_T1_to_T1_slab_registration_ants_mqc.gif:md5,e5730d99d11edfc9802776c782edbf17"
+                    ]
+                ],
+                "backward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30"
+                    ]
+                ],
+                "backward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30",
+                            "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                        ]
+                    ]
+                ],
+                "backward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe",
+                            "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                        ]
+                    ]
+                ],
+                "backward_warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                    ]
+                ],
+                "forward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                    ]
+                ],
+                "forward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe",
+                            "test_forward1_affine.mat:md5,dde4de8a1ca4ff1647e55dc1fece402c"
+                        ]
+                    ]
+                ],
+                "forward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,8cc894275b42e3b78efca499caf22e30",
+                            "test_backward1_warp.nii.gz:md5,28f58437d878a6ea0c81c0e780e2333f"
+                        ]
+                    ]
+                ],
+                "forward_warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward0_warp.nii.gz:md5,96b2d18c7537db76366e4557b44f24fe"
+                    ]
+                ],
+                "image_warped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,5534f8cb21fcc44f577d520e6083bb83"
+                    ]
+                ],
+                "mqc": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_T1_to_T1_slab_registration_ants_mqc.gif:md5,e5730d99d11edfc9802776c782edbf17"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T13:00:13.19463937"
+    },
+    "registration - ants - SyN": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,8d9c289924c4d2c8edab3feae669d1c3"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                    ]
+                ],
+                "10": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9",
+                            "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9",
+                            "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                        ]
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9",
+                            "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                        ]
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9",
+                            "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                        ]
+                    ]
+                ],
+                "9": [
+                    
+                ],
+                "backward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9"
+                    ]
+                ],
+                "backward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9",
+                            "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                        ]
+                    ]
+                ],
+                "backward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9",
+                            "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                        ]
+                    ]
+                ],
+                "backward_warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                    ]
+                ],
+                "forward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                    ]
+                ],
+                "forward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9",
+                            "test_forward1_affine.mat:md5,16a42a74c35c9fda7786250b333bef86"
+                        ]
+                    ]
+                ],
+                "forward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,317e067757768c8e75de9d12f84563c9",
+                            "test_backward1_warp.nii.gz:md5,3f2d23cce4fbcf970099eecd629d4019"
+                        ]
+                    ]
+                ],
+                "forward_warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward0_warp.nii.gz:md5,9a3b969b74ac82ab0940b8b94677c7b9"
+                    ]
+                ],
+                "image_warped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,8d9c289924c4d2c8edab3feae669d1c3"
+                    ]
+                ],
+                "mqc": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T12:58:47.595933738"
+    },
+    "registration - ants - no warps": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,c13330e3f71c57f2517dcd6f59f64ff1"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                    ]
+                ],
+                "10": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                        ]
+                    ]
+                ],
+                "6": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                        ]
+                    ]
+                ],
+                "7": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                        ]
+                    ]
+                ],
+                "8": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                        ]
+                    ]
+                ],
+                "9": [
+                    
+                ],
+                "backward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                    ]
+                ],
+                "backward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                        ]
+                    ]
+                ],
+                "backward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                        ]
+                    ]
+                ],
+                "backward_warp": [
+                    
+                ],
+                "forward_affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                    ]
+                ],
+                "forward_image_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_forward1_affine.mat:md5,7387bc8f93dd29d2a0aadb9d5dc06d5b"
+                        ]
+                    ]
+                ],
+                "forward_tractogram_transform": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        [
+                            "test_backward0_affine.mat:md5,733babe33e1656d0f85064caf24d6f82"
+                        ]
+                    ]
+                ],
+                "forward_warp": [
+                    
+                ],
+                "image_warped": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_t1_warped.nii.gz:md5,c13330e3f71c57f2517dcd6f59f64ff1"
+                    ]
+                ],
+                "mqc": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,78610891ed0adf1a5fe5f0de034d7555"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.0"
+        },
+        "timestamp": "2025-10-28T13:00:29.996790917"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/nextflow.config b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow.config
new file mode 100644
index 00000000..4c2ce76e
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+    withName: "REGISTRATION_COBRALABANTS" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.repro_mode = 1
+        ext.initial_transform = "com"
+    }
+}
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_no_warp.config b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_no_warp.config
new file mode 100644
index 00000000..e63042d6
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_no_warp.config
@@ -0,0 +1,8 @@
+process {
+    withName: "REGISTRATION_COBRALABANTS" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.fast = true
+        ext.skip_nonlinear = true
+        ext.ext.linear_type = 'rigid'
+    }
+}
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_quick.config b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_quick.config
new file mode 100644
index 00000000..349e46c9
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/nextflow_quick.config
@@ -0,0 +1,8 @@
+process {
+    withName: "REGISTRATION_COBRALABANTS" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.fast = true
+        ext.run_qc = true
+        ext.suffix_qc = "T1_to_T1_slab"
+    }
+}
diff --git a/modules/nf-neuro/registration/cobralab_ants/tests/tags.yml b/modules/nf-neuro/registration/cobralab_ants/tests/tags.yml
new file mode 100644
index 00000000..8aa857e3
--- /dev/null
+++ b/modules/nf-neuro/registration/cobralab_ants/tests/tags.yml
@@ -0,0 +1,2 @@
+registration/ants:
+  - "modules/nf-neuro/registration/ants/**"