diff --git a/modules/nf-neuro/registration/anattodwi/main.nf b/modules/nf-neuro/registration/anattodwi/main.nf
index 8e4e745b..f0aaaac8 100644
--- a/modules/nf-neuro/registration/anattodwi/main.nf
+++ b/modules/nf-neuro/registration/anattodwi/main.nf
@@ -2,9 +2,7 @@ process REGISTRATION_ANATTODWI {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:19c87b72bcbc683fb827097dda7f917940fda123' }"
+    container "scilus/scilus:2.2.0"
 
     input:
     tuple val(meta), path(t1), path(b0), path(metric)
@@ -73,11 +71,11 @@ process REGISTRATION_ANATTODWI {
         # Iterate over images.
         for image in t1_warped b0;
         do
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_coronal.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_coronal.png \
                 --slices \$coronal_mid --axis coronal \$viz_params
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_sagittal.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_sagittal.png \
                 --slices \$sagittal_mid --axis sagittal \$viz_params
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_axial.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_axial.png \
                 --slices \$axial_mid --axis axial \$viz_params
 
             if [ \$image != b0 ];
@@ -107,6 +105,7 @@ process REGISTRATION_ANATTODWI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | sed -n 's/.*ImageMagick \\([0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\).*/\\1/p')
@@ -117,7 +116,17 @@ process REGISTRATION_ANATTODWI {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
+    set +e
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    [[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
+    }
+    trap 'handle_code' ERR
+
     antsRegistration -h
+    scil_viz_volume_screenshot -h
+    convert -h
 
     touch ${prefix}__t1_warped.nii.gz
     touch ${prefix}__output0GenericAffine.mat
@@ -127,6 +136,7 @@ process REGISTRATION_ANATTODWI {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | sed -n 's/.*ImageMagick \\([0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\.[0-9]\\{1,\\}\\).*/\\1/p')
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 aebfc5f2..86591bc5 100644
--- a/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/anattodwi/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
+                        "test__output0GenericAffine.mat:md5,18d03f6c1fd587b00b3bc9363eb8ed4f"
                     ]
                 ],
                 "1": [
@@ -17,7 +17,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
+                        "test__output1Warp.nii.gz:md5,aa42d4dd6f227d986cd99df45425d5c5"
                     ]
                 ],
                 "2": [
@@ -26,7 +26,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
+                        "test__output1InverseWarp.nii.gz:md5,6a04d7c100075b4ba7a276a55a4094bd"
                     ]
                 ],
                 "3": [
@@ -35,7 +35,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
+                        "test__t1_warped.nii.gz:md5,39c30c6251cba224989bc74a31540121"
                     ]
                 ],
                 "4": [
@@ -44,11 +44,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_registration_anattodwi_mqc.gif:md5,74a7cf404c443726487683c23bd926c0"
+                        "test_registration_anattodwi_mqc.gif:md5,687252d31b0109f99a174b4e3960e4e6"
                     ]
                 ],
                 "5": [
-                    "versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
+                    "versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
                 ],
                 "affine": [
                     [
@@ -56,7 +56,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output0GenericAffine.mat:md5,6eef07f9004fb96e57ae0404ffef174c"
+                        "test__output0GenericAffine.mat:md5,18d03f6c1fd587b00b3bc9363eb8ed4f"
                     ]
                 ],
                 "inverse_warp": [
@@ -65,7 +65,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1InverseWarp.nii.gz:md5,28694d2b41f5209ab8f1acbb219014fe"
+                        "test__output1InverseWarp.nii.gz:md5,6a04d7c100075b4ba7a276a55a4094bd"
                     ]
                 ],
                 "mqc": [
@@ -74,7 +74,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_registration_anattodwi_mqc.gif:md5,74a7cf404c443726487683c23bd926c0"
+                        "test_registration_anattodwi_mqc.gif:md5,687252d31b0109f99a174b4e3960e4e6"
                     ]
                 ],
                 "t1_warped": [
@@ -83,11 +83,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__t1_warped.nii.gz:md5,9c34f424900adea263e39ed1f37a793f"
+                        "test__t1_warped.nii.gz:md5,39c30c6251cba224989bc74a31540121"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
+                    "versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
                 ],
                 "warp": [
                     [
@@ -95,27 +95,27 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__output1Warp.nii.gz:md5,e0995852e251bee5521572a4495a0bd6"
+                        "test__output1Warp.nii.gz:md5,aa42d4dd6f227d986cd99df45425d5c5"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-02-20T14:58:42.372471"
+        "timestamp": "2025-09-22T21:23:44.360834413"
     },
     "registration - anattodwi -stub-run": {
         "content": [
             [
-                "versions.yml:md5,f368bc76bf8d1f1a68caea3597b0c65b"
+                "versions.yml:md5,77dc5dd2d9f2f2b772043eef8471eb13"
             ]
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.3"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-02-20T14:58:49.169195"
+        "timestamp": "2025-09-22T21:24:00.939016823"
     }
 }
\ 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 d12fcf53..9b16683a 100644
--- a/modules/nf-neuro/registration/ants/main.nf
+++ b/modules/nf-neuro/registration/ants/main.nf
@@ -3,9 +3,7 @@ process REGISTRATION_ANTS {
     tag "$meta.id"
     label 'process_medium'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        "https://scil.usherbrooke.ca/containers/scilus_latest.sif":
-        "scilus/scilus:19c87b72bcbc683fb827097dda7f917940fda123"}"
+    container "scilus/scilus:2.2.0"
 
     input:
     tuple val(meta), path(fixedimage), path(movingimage), path(mask) /* optional, input = [] */
@@ -80,11 +78,11 @@ process REGISTRATION_ANTS {
         # Iterate over images.
         for image in fixedimage warped;
         do
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_coronal.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_coronal.png \
                 --slices \$coronal_dim --axis coronal \$viz_params
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_sagittal.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_sagittal.png \
                 --slices \$sagittal_dim --axis sagittal \$viz_params
-            scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_axial.png \
+            scil_viz_volume_screenshot *\${image}.nii.gz \${image}_axial.png \
                 --slices \$axial_dim --axis axial \$viz_params
             if [ \$image != fixedimage ];
             then
@@ -109,6 +107,7 @@ process REGISTRATION_ANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
@@ -130,6 +129,8 @@ process REGISTRATION_ANTS {
 
     antsRegistrationSyNQuick.sh -h
     antsApplyTransforms -h
+    convert -h
+    scil_viz_volume_screenshot -h
 
     touch ${prefix}__t1_warped.nii.gz
     touch ${prefix}__output0GenericAffine.mat
@@ -139,6 +140,7 @@ process REGISTRATION_ANTS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
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 782a7ab3..c2e97b65 100644
--- a/modules/nf-neuro/registration/ants/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/ants/tests/main.nf.test.snap
@@ -7,7 +7,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,4382217c04988eb01ed8f99916d7631c"
+                        "test__warped.nii.gz:md5,6491f46d2c2cae09338effb989ec3bf7"
                     ]
                 ],
                 "1": [
@@ -15,7 +15,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
+                        "test__output0GenericAffine.mat:md5,3b6d0eaddd216d15bf50a116c2f09065"
                     ]
                 ],
                 "2": [
@@ -23,7 +23,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8"
+                        "test__output1InverseAffine.mat:md5,14b90a8217065e42b21102de73a489c1"
                     ]
                 ],
                 "3": [
@@ -31,7 +31,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17"
+                        "test__output1Warp.nii.gz:md5,db8e148adf0e32d551cf5e75ca3e76ab"
                     ]
                 ],
                 "4": [
@@ -39,21 +39,21 @@
                         {
                             "id": "test"
                         },
-                        "test__output0InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
+                        "test__output0InverseWarp.nii.gz:md5,3069b784eaa199078d21ecbd5366e27b"
                     ]
                 ],
                 "5": [
                     
                 ],
                 "6": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "affine": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,8e987eb08cc568478c37ae79a8824f8b"
+                        "test__output0GenericAffine.mat:md5,3b6d0eaddd216d15bf50a116c2f09065"
                     ]
                 ],
                 "image": [
@@ -61,7 +61,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,4382217c04988eb01ed8f99916d7631c"
+                        "test__warped.nii.gz:md5,6491f46d2c2cae09338effb989ec3bf7"
                     ]
                 ],
                 "inverse_affine": [
@@ -69,7 +69,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,d342d5f1c35a53cadcdf2d49a25f5ce8"
+                        "test__output1InverseAffine.mat:md5,14b90a8217065e42b21102de73a489c1"
                     ]
                 ],
                 "inverse_warp": [
@@ -77,30 +77,30 @@
                         {
                             "id": "test"
                         },
-                        "test__output0InverseWarp.nii.gz:md5,1608837de13478dff81fe51ac1720d28"
+                        "test__output0InverseWarp.nii.gz:md5,3069b784eaa199078d21ecbd5366e27b"
                     ]
                 ],
                 "mqc": [
                     
                 ],
                 "versions": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "warp": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output1Warp.nii.gz:md5,6fee747df2c30bb48cf2b6897b5d3e17"
+                        "test__output1Warp.nii.gz:md5,db8e148adf0e32d551cf5e75ca3e76ab"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-06-05T15:46:55.295203257"
+        "timestamp": "2025-09-22T21:59:53.198912314"
     },
     "registration - ants - quick": {
         "content": [
@@ -110,7 +110,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,81358dd2f3223f567f4101e61490ae0f"
+                        "test__warped.nii.gz:md5,45822afae6c0dc33551b690f6f10dbe4"
                     ]
                 ],
                 "1": [
@@ -118,7 +118,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
+                        "test__output0GenericAffine.mat:md5,17e711c6a2f73415269b4272344890bc"
                     ]
                 ],
                 "2": [
@@ -126,7 +126,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15"
+                        "test__output1InverseAffine.mat:md5,e5df1f989e0340746d9742ff2d0a7a99"
                     ]
                 ],
                 "3": [
@@ -134,7 +134,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                        "test__output1Warp.nii.gz:md5,813a4218d33d5acfebadc4ba0e49df8b"
                     ]
                 ],
                 "4": [
@@ -142,7 +142,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output0InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                        "test__output0InverseWarp.nii.gz:md5,813a4218d33d5acfebadc4ba0e49df8b"
                     ]
                 ],
                 "5": [
@@ -150,18 +150,18 @@
                         {
                             "id": "test"
                         },
-                        "test_T1_to_DWI_registration_ants_mqc.gif:md5,ebf58acb9c3f3b9bc8c5a08105d4ceff"
+                        "test_T1_to_DWI_registration_ants_mqc.gif:md5,9cdd7e9bf7facc3f95a61de03e15d47d"
                     ]
                 ],
                 "6": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "affine": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,48c8479a403e0c0ec29c69d37bb4c91a"
+                        "test__output0GenericAffine.mat:md5,17e711c6a2f73415269b4272344890bc"
                     ]
                 ],
                 "image": [
@@ -169,7 +169,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,81358dd2f3223f567f4101e61490ae0f"
+                        "test__warped.nii.gz:md5,45822afae6c0dc33551b690f6f10dbe4"
                     ]
                 ],
                 "inverse_affine": [
@@ -177,7 +177,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,25d0b8a83a922f2e4e89c6a86258af15"
+                        "test__output1InverseAffine.mat:md5,e5df1f989e0340746d9742ff2d0a7a99"
                     ]
                 ],
                 "inverse_warp": [
@@ -185,7 +185,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output0InverseWarp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                        "test__output0InverseWarp.nii.gz:md5,813a4218d33d5acfebadc4ba0e49df8b"
                     ]
                 ],
                 "mqc": [
@@ -193,27 +193,27 @@
                         {
                             "id": "test"
                         },
-                        "test_T1_to_DWI_registration_ants_mqc.gif:md5,ebf58acb9c3f3b9bc8c5a08105d4ceff"
+                        "test_T1_to_DWI_registration_ants_mqc.gif:md5,9cdd7e9bf7facc3f95a61de03e15d47d"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "warp": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output1Warp.nii.gz:md5,24e6f53eaa3e4476bb627c374bc809ca"
+                        "test__output1Warp.nii.gz:md5,813a4218d33d5acfebadc4ba0e49df8b"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-06-05T15:36:19.045796771"
+        "timestamp": "2025-09-22T22:00:25.806953541"
     },
     "registration - ants - options": {
         "content": [
@@ -223,7 +223,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,7cb6839d4af18d9d37a1bd9d07c8c57b"
+                        "test__warped.nii.gz:md5,c090343bdf2af2eac20a051b3cf9bb20"
                     ]
                 ],
                 "1": [
@@ -231,7 +231,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,c3a48d19c815206de2b140f505969317"
+                        "test__output0GenericAffine.mat:md5,d3230976041b8532b14a00e2e5760395"
                     ]
                 ],
                 "2": [
@@ -239,7 +239,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,f473c1e548be1540cbf757202ffd5984"
+                        "test__output1InverseAffine.mat:md5,10a6c2eededdc85709bbff395f0aab3a"
                     ]
                 ],
                 "3": [
@@ -253,18 +253,18 @@
                         {
                             "id": "test"
                         },
-                        "test__registration_ants_mqc.gif:md5,23a92899290210c2fed8dbd9ed6b946b"
+                        "test__registration_ants_mqc.gif:md5,1bfa145273f0ece8a2293efc7d2a8c2e"
                     ]
                 ],
                 "6": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "affine": [
                     [
                         {
                             "id": "test"
                         },
-                        "test__output0GenericAffine.mat:md5,c3a48d19c815206de2b140f505969317"
+                        "test__output0GenericAffine.mat:md5,d3230976041b8532b14a00e2e5760395"
                     ]
                 ],
                 "image": [
@@ -272,7 +272,7 @@
                         {
                             "id": "test"
                         },
-                        "test__warped.nii.gz:md5,7cb6839d4af18d9d37a1bd9d07c8c57b"
+                        "test__warped.nii.gz:md5,c090343bdf2af2eac20a051b3cf9bb20"
                     ]
                 ],
                 "inverse_affine": [
@@ -280,7 +280,7 @@
                         {
                             "id": "test"
                         },
-                        "test__output1InverseAffine.mat:md5,f473c1e548be1540cbf757202ffd5984"
+                        "test__output1InverseAffine.mat:md5,10a6c2eededdc85709bbff395f0aab3a"
                     ]
                 ],
                 "inverse_warp": [
@@ -291,11 +291,11 @@
                         {
                             "id": "test"
                         },
-                        "test__registration_ants_mqc.gif:md5,23a92899290210c2fed8dbd9ed6b946b"
+                        "test__registration_ants_mqc.gif:md5,1bfa145273f0ece8a2293efc7d2a8c2e"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                    "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
                 ],
                 "warp": [
                     
@@ -304,20 +304,20 @@
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-06-05T15:48:39.225501284"
+        "timestamp": "2025-09-22T22:00:54.46748032"
     },
     "registration - ants - stub": {
         "content": [
             [
-                "versions.yml:md5,2f2f86409f3c1a7fedd6a4c670fde0fa"
+                "versions.yml:md5,b79ebe5518288b629eb72580d6e6b785"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-06-05T15:47:24.380872364"
+        "timestamp": "2025-09-22T22:01:09.70219899"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-neuro/registration/antsapplytransforms/main.nf b/modules/nf-neuro/registration/antsapplytransforms/main.nf
index d48ef9ce..b4a4519d 100644
--- a/modules/nf-neuro/registration/antsapplytransforms/main.nf
+++ b/modules/nf-neuro/registration/antsapplytransforms/main.nf
@@ -2,9 +2,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
     tag "$meta.id"
     label 'process_low'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        "https://scil.usherbrooke.ca/containers/scilus_latest.sif":
-        "scilus/scilus:19c87b72bcbc683fb827097dda7f917940fda123"}"
+    container "scilus/scilus:2.2.0"
 
     input:
     tuple val(meta), path(image), path(reference), path(warp), path(affine)
@@ -66,11 +64,11 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
             # Iterate over images.
             for image in reference \${bname}${suffix};
             do
-                scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_coronal.png \
+                scil_viz_volume_screenshot *\${image}.nii.gz \${image}_coronal.png \
                     --slices \$coronal_dim --axis coronal \$viz_params
-                scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_sagittal.png \
+                scil_viz_volume_screenshot *\${image}.nii.gz \${image}_sagittal.png \
                     --slices \$sagittal_dim --axis sagittal \$viz_params
-                scil_viz_volume_screenshot.py *\${image}.nii.gz \${image}_axial.png \
+                scil_viz_volume_screenshot *\${image}.nii.gz \${image}_axial.png \
                     --slices \$axial_dim --axis axial \$viz_params
                 if [ \$image != reference ];
                 then
@@ -96,6 +94,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
@@ -107,7 +106,17 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
     def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}__warped" : "__warped"
 
     """
+    set +e
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    [[ " \${ignore[@]} " =~ " \$code " ]] || exit \$code
+    }
+    trap 'handle_code' ERR
+
     antsApplyTransforms -h
+    convert -h
+    scil_viz_volume_screenshot -h
 
     for image in $image;
         do \
@@ -119,6 +128,7 @@ process REGISTRATION_ANTSAPPLYTRANSFORMS {
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
         ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9.a-zA-Z-]+).*/\\1/')
         mrtrix: \$(mrinfo -version 2>&1 | grep "== mrinfo" | sed -E 's/== mrinfo ([0-9.]+).*/\\1/')
         imagemagick: \$(convert -version | grep "Version:" | sed -E 's/.*ImageMagick ([0-9.-]+).*/\\1/')
diff --git a/modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test.snap b/modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test.snap
index 35beb8cf..895a830a 100644
--- a/modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/antsapplytransforms/tests/main.nf.test.snap
@@ -8,7 +8,7 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__b0b0__warped.nii.gz:md5,3ae49aacab66fb2378da92155453b1be"
+                        "test__b0b0__warped.nii.gz:md5,00916b78f727d65a811774f932aa9ce7"
                     ]
                 ],
                 "1": [
@@ -17,11 +17,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_b0b0_to_template_registration_antsapplytransforms_mqc.gif:md5,2e97314c320a27e4271c960c50895dfb"
+                        "test_b0b0_to_template_registration_antsapplytransforms_mqc.gif:md5,ae5cc35a4039b08debee3c0ff21d5460"
                     ]
                 ],
                 "2": [
-                    "versions.yml:md5,9c43291bef0aa7f7d49133a0ad7c0878"
+                    "versions.yml:md5,02bece717a70a1c6a33bfa960afe9c33"
                 ],
                 "mqc": [
                     [
@@ -29,11 +29,11 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test_b0b0_to_template_registration_antsapplytransforms_mqc.gif:md5,2e97314c320a27e4271c960c50895dfb"
+                        "test_b0b0_to_template_registration_antsapplytransforms_mqc.gif:md5,ae5cc35a4039b08debee3c0ff21d5460"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,9c43291bef0aa7f7d49133a0ad7c0878"
+                    "versions.yml:md5,02bece717a70a1c6a33bfa960afe9c33"
                 ],
                 "warped_image": [
                     [
@@ -41,27 +41,27 @@
                             "id": "test",
                             "single_end": false
                         },
-                        "test__b0b0__warped.nii.gz:md5,3ae49aacab66fb2378da92155453b1be"
+                        "test__b0b0__warped.nii.gz:md5,00916b78f727d65a811774f932aa9ce7"
                     ]
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.9.2",
-            "nextflow": "24.10.5"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-03-14T18:15:20.750783"
+        "timestamp": "2025-09-22T22:10:27.902211304"
     },
     "registration - antsapplytransforms - stub-run": {
         "content": [
             [
-                "versions.yml:md5,9c43291bef0aa7f7d49133a0ad7c0878"
+                "versions.yml:md5,02bece717a70a1c6a33bfa960afe9c33"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.3"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-06-05T15:36:32.982446247"
+        "timestamp": "2025-09-22T22:10:41.210018268"
     }
-}
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/registration/tractogram/main.nf b/modules/nf-neuro/registration/tractogram/main.nf
index a44b5019..fe1a9086 100644
--- a/modules/nf-neuro/registration/tractogram/main.nf
+++ b/modules/nf-neuro/registration/tractogram/main.nf
@@ -2,9 +2,7 @@ process REGISTRATION_TRACTOGRAM {
     tag "$meta.id"
     label 'process_single'
 
-    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
-        'scilus/scilus:2.0.2' }"
+    container "scilus/scilpy:2.2.0_cpu"
 
     input:
     tuple val(meta), path(anat), path(transfo), path(tractogram), path(ref) /* optional, input = [] */, path(deformation) /* optional, input = [] */
@@ -36,16 +34,16 @@ process REGISTRATION_TRACTOGRAM {
     for tractogram in ${tractogram};
         do \
         ext=\${tractogram#*.}
-        bname=\$(basename \${tractogram} .\${ext})
+        bname=\$(basename \${tractogram} .\${ext} | sed 's/${prefix}_\\+//')
 
-        scil_tractogram_apply_transform.py \$tractogram $anat $transfo tmp.trk\
+        scil_tractogram_apply_transform \$tractogram $anat $transfo tmp.trk\
                         $in_deformation\
                         $inverse\
                         $reverse_operation\
                         $force\
                         $reference
 
-        scil_tractogram_remove_invalid.py tmp.trk ${prefix}__\${bname}${suffix}.\${ext}\
+        scil_tractogram_remove_invalid tmp.trk ${prefix}__\${bname}${suffix}.\${ext}\
                         $cut_invalid\
                         $remove_single_point\
                         $remove_overlapping_points\
@@ -54,11 +52,9 @@ process REGISTRATION_TRACTOGRAM {
                         -f
     done
 
-
-
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.2
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -66,20 +62,20 @@ process REGISTRATION_TRACTOGRAM {
     def prefix = task.ext.prefix ?: "${meta.id}"
     def suffix = task.ext.suffix ? "_${task.ext.suffix}" : ""
     """
-    scil_tractogram_apply_transform.py -h
-    scil_tractogram_remove_invalid.py -h
+    scil_tractogram_apply_transform -h
+    scil_tractogram_remove_invalid -h
 
     for tractogram in ${tractogram};
         do \
         ext=\${tractogram#*.}
-        bname=\$(basename \${tractogram} .\${ext})
+        bname=\$(basename \${tractogram} .\${ext} | sed 's/${prefix}_\\+//')
 
         touch ${prefix}__\${bname}${suffix}.\${ext}
     done
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
-        scilpy: 2.0.2
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-neuro/registration/tractogram/tests/main.nf.test.snap b/modules/nf-neuro/registration/tractogram/tests/main.nf.test.snap
index fb2a8cb9..b3172550 100644
--- a/modules/nf-neuro/registration/tractogram/tests/main.nf.test.snap
+++ b/modules/nf-neuro/registration/tractogram/tests/main.nf.test.snap
@@ -20,10 +20,10 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                    "versions.yml:md5,504210d056544efae377411b749443e5"
                 ],
                 "versions": [
-                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                    "versions.yml:md5,504210d056544efae377411b749443e5"
                 ],
                 "warped_tractogram": [
                     [
@@ -45,22 +45,22 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-05-15T19:11:42.198039"
+        "timestamp": "2025-09-22T22:17:00.981071105"
     },
     "registration - tractogram - stub-run": {
         "content": [
             [
-                "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                "versions.yml:md5,504210d056544efae377411b749443e5"
             ]
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.2"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-05-30T18:56:28.652442885"
+        "timestamp": "2025-09-22T22:17:25.469054766"
     },
     "registration - tractogram": {
         "content": [
@@ -75,10 +75,10 @@
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                    "versions.yml:md5,504210d056544efae377411b749443e5"
                 ],
                 "versions": [
-                    "versions.yml:md5,609469c08e60062eed7528276deddf5e"
+                    "versions.yml:md5,504210d056544efae377411b749443e5"
                 ],
                 "warped_tractogram": [
                     [
@@ -92,9 +92,9 @@
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0",
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2024-05-15T19:11:52.03634"
+        "timestamp": "2025-09-22T22:17:13.547090754"
     }
 }
\ No newline at end of file
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 a78d4c6a..5a991a52 100644
--- a/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/bundle_seg/tests/main.nf.test.snap
@@ -11,8 +11,8 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,2fbc09a51203e509d1a15a631168680e",
-                    "versions.yml:md5,afaf6c2953accc507d8777303eea8718"
+                    "versions.yml:md5,afaf6c2953accc507d8777303eea8718",
+                    "versions.yml:md5,e9075cd2c5d1ac7fa7946d2def1b66ad"
                 ]
             }
         ],
@@ -20,6 +20,6 @@
             "nf-test": "0.9.0",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-21T20:16:54.243026235"
+        "timestamp": "2025-09-23T01:31:10.284602495"
     }
 }
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/output_template_space/tests/main.nf.test.snap b/subworkflows/nf-neuro/output_template_space/tests/main.nf.test.snap
index 7637ed71..52b9556d 100644
--- a/subworkflows/nf-neuro/output_template_space/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/output_template_space/tests/main.nf.test.snap
@@ -45,11 +45,11 @@
                 "versions": [
                     "versions.yml:md5,00dee5d05eb6c7fa693b718e2264ce48",
                     "versions.yml:md5,08c023826481c9130c3914096cda7f63",
-                    "versions.yml:md5,4aa75761841b81efa97cd28be409ead9",
+                    "versions.yml:md5,392b8d0b7b937f27fd6d8433d5b00618",
+                    "versions.yml:md5,45b571aa920458a8bb0b39343c863604",
                     "versions.yml:md5,4fe062075b77eb5fd05e956d9da383c8",
-                    "versions.yml:md5,a6b014172fd4dfe073bb793b58943c46",
-                    "versions.yml:md5,e667d19be259b1983b4451f18751d3b8",
-                    "versions.yml:md5,f131337fe390b5d6c58ab1f1223bd4e8"
+                    "versions.yml:md5,a8806981919b9cc22e2e1b374119a4e6",
+                    "versions.yml:md5,c26daff464d53300427f71a85be86552"
                 ]
             }
         ],
@@ -57,7 +57,7 @@
             "nf-test": "0.9.0",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T20:06:30.618698443"
+        "timestamp": "2025-09-22T22:03:12.493670596"
     },
     "output to template MNI152NLin2009cAsym with local folder": {
         "content": [
@@ -105,11 +105,11 @@
                 "versions": [
                     "versions.yml:md5,00dee5d05eb6c7fa693b718e2264ce48",
                     "versions.yml:md5,08c023826481c9130c3914096cda7f63",
-                    "versions.yml:md5,4aa75761841b81efa97cd28be409ead9",
+                    "versions.yml:md5,392b8d0b7b937f27fd6d8433d5b00618",
+                    "versions.yml:md5,45b571aa920458a8bb0b39343c863604",
                     "versions.yml:md5,4fe062075b77eb5fd05e956d9da383c8",
-                    "versions.yml:md5,a6b014172fd4dfe073bb793b58943c46",
-                    "versions.yml:md5,e667d19be259b1983b4451f18751d3b8",
-                    "versions.yml:md5,f131337fe390b5d6c58ab1f1223bd4e8"
+                    "versions.yml:md5,a8806981919b9cc22e2e1b374119a4e6",
+                    "versions.yml:md5,c26daff464d53300427f71a85be86552"
                 ]
             }
         ],
@@ -117,6 +117,6 @@
             "nf-test": "0.9.0",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-17T20:06:16.771618815"
+        "timestamp": "2025-09-22T22:02:39.128580348"
     }
-}
+}
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/registration/tests/main.nf.test.snap b/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
index 09beaa34..8d2a1378 100644
--- a/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/registration/tests/main.nf.test.snap
@@ -122,15 +122,15 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,04d2203fd83e0422e103384bee7a1696"
+                    "versions.yml:md5,8805896edb4405a6c415e94796cc4853"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-07-04T20:59:34.81185618"
+        "timestamp": "2025-09-22T21:24:20.046469568"
     },
     "registration - SyNQuick": {
         "content": [
@@ -162,14 +162,14 @@
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,806ff315748e1402954ef52cadb7e396"
+                    "versions.yml:md5,8b28f474ec25bfa9df8abedbe6bce396"
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.0",
-            "nextflow": "25.04.6"
+            "nextflow": "25.04.7"
         },
-        "timestamp": "2025-07-04T20:59:41.187983313"
+        "timestamp": "2025-09-22T21:24:36.51483224"
     }
-}
+}
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap
index e82f0966..bc3d35f0 100644
--- a/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap
+++ b/subworkflows/nf-neuro/tractoflow/tests/main.nf.test.snap
@@ -383,8 +383,8 @@
                     "versions.yml:md5,7cabc91ec64b5e824e9b8f60d7dcf930",
                     "versions.yml:md5,87e7cf85066fe87ee04330852a18b9a2",
                     "versions.yml:md5,955e704dfd97848e196333d0cecf0451",
-                    "versions.yml:md5,9ec2ceb761ab4faf9c19e46d7aa201c9",
                     "versions.yml:md5,b365d463ddf58fc7b47cd51c70876a11",
+                    "versions.yml:md5,cf44274c03f2da41cdfa50966ff751a2",
                     "versions.yml:md5,da10c87dbb2ad07aa8bbf89a0c172a60"
                 ],
                 "volume_fraction": [
@@ -425,6 +425,6 @@
             "nf-test": "0.9.0",
             "nextflow": "25.04.7"
         },
-        "timestamp": "2025-09-24T03:23:27.123874216"
+        "timestamp": "2025-09-24T15:26:35.880061767"
     }
 }
\ No newline at end of file