diff --git a/modules/nf-neuro/registration/anattodwi/main.nf b/modules/nf-neuro/registration/anattodwi/main.nf
index 407d9ad3..274a6f28 100644
--- a/modules/nf-neuro/registration/anattodwi/main.nf
+++ b/modules/nf-neuro/registration/anattodwi/main.nf
@@ -10,8 +10,9 @@ process REGISTRATION_ANATTODWI {
     tuple val(meta), path(t1), path(b0), path(metric)
 
     output:
-    tuple val(meta), path("*0GenericAffine.mat"), path("*1InverseWarp.nii.gz")  , emit: transfo_trk
-    tuple val(meta), path("*1Warp.nii.gz"), path("*0GenericAffine.mat")         , emit: transfo_image
+    tuple val(meta), path("*0GenericAffine.mat")                                , emit: affine
+    tuple val(meta), path("*1Warp.nii.gz")                                      , emit: warp
+    tuple val(meta), path("*1InverseWarp.nii.gz")                               , emit: inverse_warp
     tuple val(meta), path("*t1_warped.nii.gz")                                  , emit: t1_warped
     path "versions.yml"                                                         , emit: versions
 
diff --git a/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap b/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
index 10a86b20..108fe168 100644
--- a/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
@@ -8,8 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
-                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
+                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
                     ]
                 ],
                 "1": [
@@ -18,8 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
+                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
                     ]
                 ],
                 "2": [
@@ -28,13 +26,10 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
+                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
-                ],
-                "t1_warped": [
                     [
                         {
                             "id": "test",
@@ -43,35 +38,54 @@
                         "test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
                     ]
                 ],
-                "transfo_image": [
+                "4": [
+                    "versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
+                ],
+                "affine": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
                         "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
                     ]
                 ],
-                "transfo_trk": [
+                "inverse_warp": [
                     [
                         {
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
                         "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
                     ]
                 ],
+                "t1_warped": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
+                    ]
+                ],
                 "versions": [
                     "versions.yml:md5,3b94092e010fc0f6bf505074a393ddcc"
+                ],
+                "warp": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T17:16:41.404087811"
+        "timestamp": "2024-12-16T17:41:00.965919497"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/registration/ants/main.nf b/modules/nf-neuro/registration/ants/main.nf
index 05315461..7fe75b0c 100644
--- a/modules/nf-neuro/registration/ants/main.nf
+++ b/modules/nf-neuro/registration/ants/main.nf
@@ -12,8 +12,10 @@ process REGISTRATION_ANTS {
 
     output:
     tuple val(meta), path("*_warped.nii.gz")                                  , emit: image
-    tuple val(meta), path("*__output{0Warp.nii.gz,1GenericAffine.mat}")       , emit: transfo_image
-    tuple val(meta), path("*__output{0,1}Inverse{Warp.nii.gz,Affine.mat}")    , emit: transfo_trk
+    tuple val(meta), path("*__output0Warp.nii.gz")                            , emit: warp, optional:true
+    tuple val(meta), path("*__output1GenericAffine.mat")                            , emit: affine
+    tuple val(meta), path("*__output1InverseWarp.nii.gz")                     , emit: inverse_warp, optional: true
+    tuple val(meta), path("*__output0InverseAffine.mat")                     , emit: inverse_affine
     path "versions.yml"                                                       , emit: versions
 
     when:
@@ -62,7 +64,7 @@ process REGISTRATION_ANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 
@@ -82,7 +84,7 @@ process REGISTRATION_ANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        ants: antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/'
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/registration/ants/tests/main.nf.test.snap b/modules/nf-neuro/registration/ants/tests/main.nf.test.snap
index 6f15a868..26091507 100644
--- a/modules/nf-neuro/registration/ants/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/ants/tests/main.nf.test.snap
@@ -15,10 +15,7 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17",
-                            "test__output1GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
-                        ]
+                        "test__output0Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17"
                     ]
                 ],
                 "2": [
@@ -26,14 +23,35 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8",
-                            "test__output1InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
-                        ]
+                        "test__output1GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output1InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output0InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
+                ],
+                "affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output1GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
+                    ]
                 ],
                 "image": [
                     [
@@ -43,38 +61,40 @@
                         "test__warped.nii.gz:md5,4382217c04988eb01ed8f99916d7631c"
                     ]
                 ],
-                "transfo_image": [
+                "inverse_affine": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17",
-                            "test__output1GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
-                        ]
+                        "test__output0InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8"
                     ]
                 ],
-                "transfo_trk": [
+                "inverse_warp": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8",
-                            "test__output1InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
-                        ]
+                        "test__output1InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
+                ],
+                "warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output0Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-25T17:37:35.205440745"
+        "timestamp": "2024-12-16T17:28:39.126053758"
     },
     "registration - ants - quick": {
         "content": [
@@ -92,10 +112,7 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca",
-                            "test__output1GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
-                        ]
+                        "test__output0Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
                     ]
                 ],
                 "2": [
@@ -103,14 +120,35 @@
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15",
-                            "test__output1InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
-                        ]
+                        "test__output1GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output1InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output0InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15"
+                    ]
+                ],
+                "5": [
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
+                ],
+                "affine": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output1GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
+                    ]
                 ],
                 "image": [
                     [
@@ -120,38 +158,40 @@
                         "test__warped.nii.gz:md5,81358dd2f3223f567f4101e61490ae0f"
                     ]
                 ],
-                "transfo_image": [
+                "inverse_affine": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca",
-                            "test__output1GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
-                        ]
+                        "test__output0InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15"
                     ]
                 ],
-                "transfo_trk": [
+                "inverse_warp": [
                     [
                         {
                             "id": "test"
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15",
-                            "test__output1InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
-                        ]
+                        "test__output1InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
+                ],
+                "warp": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__output0Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                    ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-25T17:14:19.681843788"
+        "timestamp": "2024-12-16T17:28:48.93660183"
     },
     "registration - ants - options": {
         "content": [
@@ -165,6 +205,9 @@
                     ]
                 ],
                 "1": [
+                    
+                ],
+                "2": [
                     [
                         {
                             "id": "test"
@@ -172,7 +215,10 @@
                         "test__output1GenericAffine.mat:md5,c3a48d19c815206de2b140f505969317"
                     ]
                 ],
-                "2": [
+                "3": [
+                    
+                ],
+                "4": [
                     [
                         {
                             "id": "test"
@@ -180,42 +226,48 @@
                         "test__output0InverseAffine.mat:md5,f473c1e548be1540cbf757202ffd5984"
                     ]
                 ],
-                "3": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                "5": [
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
                 ],
-                "image": [
+                "affine": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,7cb6839d4af18d9d37a1bd9d07c8c57b"
+                        "test__output1GenericAffine.mat:md5,c3a48d19c815206de2b140f505969317"
                     ]
                 ],
-                "transfo_image": [
+                "image": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output1GenericAffine.mat:md5,c3a48d19c815206de2b140f505969317"
+                        "test__warped.nii.gz:md5,7cb6839d4af18d9d37a1bd9d07c8c57b"
                     ]
                 ],
-                "transfo_trk": [
+                "inverse_affine": [
                     [
                         {
                             "id": "test"
                         },
                         "test__output0InverseAffine.mat:md5,f473c1e548be1540cbf757202ffd5984"
                     ]
+                ],
+                "inverse_warp": [
+                    
                 ],
                 "versions": [
-                    "versions.yml:md5,825e9d4ea9e26675d7e236f243d73114"
+                    "versions.yml:md5,e1ac7994c0f0169d932e94c6e97a4894"
+                ],
+                "warp": [
+                    
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-25T17:14:25.782091391"
+        "timestamp": "2024-12-16T17:28:54.754431506"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/registration/synthregistration/main.nf b/modules/nf-neuro/registration/synthregistration/main.nf
index 52cabf43..ed068eef 100644
--- a/modules/nf-neuro/registration/synthregistration/main.nf
+++ b/modules/nf-neuro/registration/synthregistration/main.nf
@@ -2,22 +2,22 @@ process REGISTRATION_SYNTHREGISTRATION {
     tag "$meta.id"
     label 'process_high'
 
-    container "freesurfer/synthmorph:3"
+    container "freesurfer/synthmorph:4"
     containerOptions "--entrypoint '' --env PYTHONPATH='/freesurfer/env/lib/python3.11/site-packages'"
 
     input:
     tuple val(meta), path(moving), path(fixed)
 
     output:
-    tuple val(meta), path("*__output_warped.nii.gz")                                , emit: warped_image
-    tuple val(meta), path("*__deform_warp.nii.gz"), path("*__affine_warp.lta")      , emit: transfo_image
-    path "versions.yml"           , emit: versions
+    tuple val(meta), path("*__output_warped.nii.gz")        , emit: warped_image
+    tuple val(meta), path("*__deform_warp.nii.gz")          , emit: warp
+    tuple val(meta), path("*__affine_warp.lta")             , emit: affine
+    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 affine = task.ext.affine ? "-m " + task.ext.affine : "-m affine"
@@ -39,12 +39,11 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        synthmoprh: 3
+        synthmoprh: 4
     END_VERSIONS
     """
 
     stub:
-    def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
@@ -56,7 +55,7 @@ process REGISTRATION_SYNTHREGISTRATION {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        synthmoprh: 3
+        synthmoprh: 4
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test
index 1c343caf..33dfb385 100644
--- a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test
+++ b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test
@@ -46,7 +46,8 @@ nextflow_process {
                 { assert process.success },
                 { assert snapshot(
                     file(process.out.warped_image.get(0).get(1)).name,
-                    file(process.out.transfo_image.get(0).get(1)).name,
+                    file(process.out.warp.get(0).get(1)).name,
+                    file(process.out.affine.get(0).get(1)).name,
                     process.out.versions
                 ).match() }
             )
diff --git a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap
index 23e10804..b87940b8 100644
--- a/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/synthregistration/tests/main.nf.test.snap
@@ -3,14 +3,15 @@
         "content": [
             "test__output_warped.nii.gz",
             "test__deform_warp.nii.gz",
+            "test__affine_warp.lta",
             [
-                "versions.yml:md5,5140205cdb117e3eb8cd4e28277f9291"
+                "versions.yml:md5,6f946408922f25f1a8182d35615b6d7b"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nf-test": "0.9.2",
+            "nextflow": "24.04.3"
         },
-        "timestamp": "2024-10-30T18:08:53.765658701"
+        "timestamp": "2024-12-18T13:10:28.733204"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/bundle_seg/main.nf b/subworkflows/nf-neuro/bundle_seg/main.nf
index 68b3432d..37b4bd13 100644
--- a/subworkflows/nf-neuro/bundle_seg/main.nf
+++ b/subworkflows/nf-neuro/bundle_seg/main.nf
@@ -59,14 +59,16 @@ workflow BUNDLE_SEG {
 
         // ** Setting up Atlas reference channels. ** //
         if ( params.atlas_directory ) {
-            atlas_anat = Channel.fromPath("$atlas_directory/atlas/mni_masked.nii.gz")
-            atlas_config = Channel.fromPath("$atlas_directory/config/config_fss_1.json")
-            atlas_average = Channel.fromPath("$atlas_directory/atlas/atlas/")
+            atlas_anat = Channel.fromPath("$params.atlas_directory/atlas/mni_masked.nii.gz", checkIfExists: true, relative: true)
+            atlas_config = Channel.fromPath("$params.atlas_directory/config/config_fss_1.json", checkIfExists: true, relative: true)
+            atlas_average = Channel.fromPath("$params.atlas_directory/atlas/atlas/", checkIfExists: true, relative: true)
         }
         else {
+            if ( !file("$workflow.workDir/atlas/mni_masked.nii.gz").exists() ) {
             fetch_bundleseg_atlas(  "https://zenodo.org/records/10103446/files/atlas.zip?download=1",
                                     "https://zenodo.org/records/10103446/files/config.zip?download=1",
                                     "${workflow.workDir}/")
+            }
             atlas_anat = Channel.fromPath("$workflow.workDir/atlas/mni_masked.nii.gz")
             atlas_config = Channel.fromPath("$workflow.workDir/config/config_fss_1.json")
             atlas_average = Channel.fromPath("$workflow.workDir/atlas/atlas/")
@@ -81,9 +83,10 @@ workflow BUNDLE_SEG {
         ch_versions = ch_versions.mix(REGISTRATION_ANTS.out.versions.first())
 
         // ** Perform bundle recognition and segmentation ** //
-        ch_recognize_bundle =  ch_tractogram.join(REGISTRATION_ANTS.out.transfo_image)
-                                            .combine(atlas_config)
-                                            .combine(atlas_average)
+        ch_recognize_bundle = ch_tractogram
+            .join(REGISTRATION_ANTS.out.affine)
+            .combine(atlas_config)
+            .combine(atlas_average)
 
         BUNDLE_RECOGNIZE ( ch_recognize_bundle )
         ch_versions = ch_versions.mix(BUNDLE_RECOGNIZE.out.versions.first())
diff --git a/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap b/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap
index 8fd45e33..d39b91cd 100644
--- a/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap
@@ -29,7 +29,7 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,b5ff3e60063810aea9f911b2a439b592",
+                    "versions.yml:md5,0e994f9824f1e014fd5e939e0bce7061",
                     "versions.yml:md5,e63f6133bb2e78ce211054111993be59"
                 ],
                 "bundles": [
@@ -59,15 +59,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,b5ff3e60063810aea9f911b2a439b592",
+                    "versions.yml:md5,0e994f9824f1e014fd5e939e0bce7061",
                     "versions.yml:md5,e63f6133bb2e78ce211054111993be59"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-10-24T20:26:57.178201"
+        "timestamp": "2024-12-16T17:29:39.203098281"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/registration/main.nf b/subworkflows/nf-neuro/registration/main.nf
index 05b11bea..be99659b 100644
--- a/subworkflows/nf-neuro/registration/main.nf
+++ b/subworkflows/nf-neuro/registration/main.nf
@@ -66,7 +66,8 @@ workflow REGISTRATION {
 
             // ** Set outputs ** //
             image_warped = REGISTRATION_SYNTHREGISTRATION.out.warped_image
-            transfo_image = REGISTRATION_SYNTHREGISTRATION.out.transfo_image
+            transfo_image = REGISTRATION_SYNTHREGISTRATION.out.warp
+                .join(REGISTRATION_SYNTHREGISTRATION.out.affine)
             transfo_trk = Channel.empty()
             ref_warped = Channel.empty()
             out_segmentation = Channel.empty()
@@ -97,8 +98,10 @@ workflow REGISTRATION {
 
             // ** Set compulsory outputs ** //
             image_warped = REGISTRATION_ANATTODWI.out.t1_warped
-            transfo_image = REGISTRATION_ANATTODWI.out.transfo_image
-            transfo_trk = REGISTRATION_ANATTODWI.out.transfo_trk
+            transfo_image = REGISTRATION_ANATTODWI.out.warp
+                .join(REGISTRATION_ANATTODWI.out.affine)
+            transfo_trk = REGISTRATION_ANATTODWI.out.affine
+                .join(REGISTRATION_ANATTODWI.out.inverse_warp)
 
             // ** Registration using ANTS SYN SCRIPTS ** //
             // Registration using antsRegistrationSyN.sh or antsRegistrationSyNQuick.sh, has
@@ -116,8 +119,10 @@ workflow REGISTRATION {
 
             // ** Set compulsory outputs ** //
             image_warped = image_warped.mix(REGISTRATION_ANTS.out.image)
-            transfo_image = transfo_image.mix(REGISTRATION_ANTS.out.transfo_image)
-            transfo_trk = transfo_trk.mix(REGISTRATION_ANTS.out.transfo_trk)
+            transfo_image = transfo_image.mix(REGISTRATION_ANTS.out.warp)
+                .join(REGISTRATION_ANTS.out.affine)
+            transfo_trk = transfo_trk.mix(REGISTRATION_ANTS.out.inverse_affine)
+                .join(REGISTRATION_ANTS.out.inverse_warp)
 
             // **et optional outputs **//
             ref_warped = Channel.empty()
@@ -128,8 +133,8 @@ workflow REGISTRATION {
     emit:
         image_warped        = image_warped            // channel: [ val(meta), image ] ]
         ref_warped          = ref_warped              // channel: [ val(meta), ref ]
-        transfo_image       = transfo_image           // channel: [ val(meta), [ warp, <affine> ] ]
-        transfo_trk         = transfo_trk             // channel: [ val(meta), [ <inverse-affine>, inverse-warp ] ]
+        transfo_image       = transfo_image           // channel: [ val(meta), [ warp ], [ <affine> ] ]
+        transfo_trk         = transfo_trk             // channel: [ val(meta), [ <inverse-affine> ], [ inverse-warp ] ]
         segmentation        = out_segmentation        // channel: [ val(meta), segmentation ]
         ref_segmentation    = out_ref_segmentation    // channel: [ val(meta), ref-segmentation ]
         versions            = ch_versions             // channel: [ versions.yml ]
diff --git a/subworkflows/nf-neuro/registration/tests/main.nf.test.snap b/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
index cb402dde..c3f7dbc5 100644
--- a/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
@@ -47,24 +47,10 @@
                     
                 ],
                 "2": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
-                    ]
+                    
                 ],
                 "3": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
-                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
-                    ]
+                    
                 ],
                 "4": [
                     
@@ -94,24 +80,10 @@
                     
                 ],
                 "transfo_image": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6",
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
-                    ]
+                    
                 ],
                 "transfo_trk": [
-                    [
-                        {
-                            "id": "test",
-                            "single_end": false
-                        },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c",
-                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
-                    ]
+                    
                 ],
                 "versions": [
                     "versions.yml:md5,9c255f4c751382be7bf6fe6ffb0d635d"
@@ -120,9 +92,9 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "24.04.4"
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-11-22T17:18:54.515678597"
+        "timestamp": "2024-12-16T17:18:27.440150515"
     },
     "registration - SyNQuick": {
         "content": [
@@ -145,10 +117,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,964cf7e60171214164f280452f1ae6e0",
-                            "test__output1GenericAffine.mat:md5,bfd589d2b237a20bbeef0656ecd64e14"
-                        ]
+                        "test__output0Warp.nii.gz:md5,964cf7e60171214164f280452f1ae6e0",
+                        "test__output1GenericAffine.mat:md5,bfd589d2b237a20bbeef0656ecd64e14"
                     ]
                 ],
                 "3": [
@@ -157,10 +127,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,235417a8c7eee8ab7bde320b9e48d2f1",
-                            "test__output1InverseWarp.nii.gz:md5,fac9af1885f5e1cce39fcf06fca93dfc"
-                        ]
+                        "test__output0InverseAffine.mat:md5,235417a8c7eee8ab7bde320b9e48d2f1",
+                        "test__output1InverseWarp.nii.gz:md5,fac9af1885f5e1cce39fcf06fca93dfc"
                     ]
                 ],
                 "4": [
@@ -170,7 +138,7 @@
                     
                 ],
                 "6": [
-                    "versions.yml:md5,9fe7f597ac6c76efff8851f9b672f17b"
+                    "versions.yml:md5,96376b8bc28640eef565e7f1e258dbb2"
                 ],
                 "image_warped": [
                     [
@@ -196,10 +164,8 @@
                             "id": "test",
                             "single_end": false
                         },
-                        [
-                            "test__output0Warp.nii.gz:md5,964cf7e60171214164f280452f1ae6e0",
-                            "test__output1GenericAffine.mat:md5,bfd589d2b237a20bbeef0656ecd64e14"
-                        ]
+                        "test__output0Warp.nii.gz:md5,964cf7e60171214164f280452f1ae6e0",
+                        "test__output1GenericAffine.mat:md5,bfd589d2b237a20bbeef0656ecd64e14"
                     ]
                 ],
                 "transfo_trk": [
@@ -208,21 +174,19 @@
                             "id": "test",
                             "single_end": false
                         },
-                        [
-                            "test__output0InverseAffine.mat:md5,235417a8c7eee8ab7bde320b9e48d2f1",
-                            "test__output1InverseWarp.nii.gz:md5,fac9af1885f5e1cce39fcf06fca93dfc"
-                        ]
+                        "test__output0InverseAffine.mat:md5,235417a8c7eee8ab7bde320b9e48d2f1",
+                        "test__output1InverseWarp.nii.gz:md5,fac9af1885f5e1cce39fcf06fca93dfc"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9fe7f597ac6c76efff8851f9b672f17b"
+                    "versions.yml:md5,96376b8bc28640eef565e7f1e258dbb2"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.04.3"
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
         },
-        "timestamp": "2024-12-04T13:19:52.734589"
+        "timestamp": "2024-12-16T17:32:06.600864666"
     }
 }
\ No newline at end of file