diff --git a/.github/workflows/nf-test_module.yml b/.github/workflows/nf-test_module.yml
index 2993eed7..cb86865c 100644
--- a/.github/workflows/nf-test_module.yml
+++ b/.github/workflows/nf-test_module.yml
@@ -76,16 +76,16 @@ jobs:
             ${{ runner.os }}-pip-pdiff
 
       - uses: actions/github-script@v7
-        id: test-data-cache-key
+        id: test-run-identifier
         with:
           script: |
             identifier='${{ inputs.paths }}'.toLowerCase().replaceAll(/[/. ]+/g, '-').trim('-');
-            core.setOutput('key', identifier);
+            core.setOutput('tag', identifier);
 
       - uses: actions/cache@v4
         with:
           path: ${{ env.NFSCIL_TEST_DATA_HOME }}/nf-scil-test-archives
-          key: nf-scil-test-data-cache-${{ steps.test-data-cache-key.outputs.key }}
+          key: nf-scil-test-data-cache-${{ steps.test-run-identifier.outputs.tag }}
 
       - name: Install Python dependencies
         run: python -m pip install --upgrade pip pdiff cryptography
@@ -112,6 +112,7 @@ jobs:
             --profile=$PROFILE \
             --tap=test.tap \
             --verbose \
+            --debug \
             ${{ inputs.paths }}
 
       - uses: pcolby/tap-summary@v1
@@ -119,6 +120,28 @@ jobs:
           path: >-
             test.tap
 
+      - name: Tests logs
+        if: failure()
+        run: |
+            shopt -s globstar
+            for f in /home/runner/_work/tests/**/work/**/.command.log
+            do
+
+            echo "$(sed '3q;d' $(dirname $f)/.command.run)"
+            cat $f
+
+            done
+
+      - name: Upload images as artifacts
+        if: always()
+        uses: actions/upload-artifact@v4
+        with:
+          name: image_artifacts-${{ steps.test-run-identifier.outputs.tag }}
+          path: /home/runner/_work/tests/**/work/**/*.nii.gz
+          overwrite: true
+          retention-days: 2
+          compression-level: 9
+
       - name: Clean up
         if: always()
         run: |
diff --git a/modules/nf-scil/denoising/mppca/main.nf b/modules/nf-scil/denoising/mppca/main.nf
index b7b22fe8..ce742f22 100755
--- a/modules/nf-scil/denoising/mppca/main.nf
+++ b/modules/nf-scil/denoising/mppca/main.nf
@@ -4,11 +4,11 @@ process DENOISING_MPPCA {
     label 'process_single'
 
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://scil.usherbrooke.ca/containers/scilus_2.0.0.sif':
-        'scilus/scilus:2.0.0' }"
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
 
     input:
-    tuple val(meta), path(dwi)
+    tuple val(meta), path(dwi), path(mask)
 
     output:
     tuple val(meta), path("*_dwi_denoised.nii.gz")  , emit: image
@@ -20,19 +20,23 @@ process DENOISING_MPPCA {
     script:
     def prefix = task.ext.prefix ?: "${meta.id}"
     def extent = task.ext.extent ? "-extent " + task.ext.extent : ""
+    def args = ["-nthreads ${task.cpus - 1}"]
+    if (mask) args += ["-mask $mask"]
 
     """
     export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
     export OMP_NUM_THREADS=1
     export OPENBLAS_NUM_THREADS=1
+    export MRTRIX_RNG_SEED=12345
 
-    dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent -nthreads 1
-    fslmaths ${prefix}_dwi_denoised.nii.gz -thr 0 ${prefix}_dwi_denoised.nii.gz
+    dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")} -debug
+    scil_volume_math.py lower_clip ${prefix}_dwi_denoised.nii.gz 0 \
+        ${prefix}_dwi_denoised.nii.gz -f
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 
@@ -49,7 +53,7 @@ process DENOISING_MPPCA {
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
-        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
     END_VERSIONS
     """
 }
diff --git a/modules/nf-scil/denoising/mppca/tests/main.nf.test b/modules/nf-scil/denoising/mppca/tests/main.nf.test
index 067b2424..5f8c55e9 100644
--- a/modules/nf-scil/denoising/mppca/tests/main.nf.test
+++ b/modules/nf-scil/denoising/mppca/tests/main.nf.test
@@ -20,7 +20,7 @@ nextflow_process {
                 script "../../../../../subworkflows/nf-scil/load_test_data/main.nf"
                 process {
                     """
-                    input[0] = Channel.from( [ "heavy.zip" ] )
+                    input[0] = Channel.from( [ "raw_DWIss300-dir8.zip", "raw_segmentation.zip" ] )
                     input[1] = "test.load-test-data"
                     """
                 }
@@ -30,12 +30,25 @@ nextflow_process {
         when {
             process {
                 """
-                input[0] = LOAD_DATA.out.test_data_directory.map{
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        dwi: it.simpleName == "raw_DWIss300-dir8"
+                        segmentation: it.simpleName == "raw_segmentation"
+                    }
+                ch_dwi = ch_split_test_data.dwi.map{
                     test_data_directory -> [
-                        [ id:'test', single_end:false ], // meta map
-                        file("\${test_data_directory}/dwi/dwi.nii.gz")
+                        [ id:'test' ],
+                        file("\${test_data_directory}/dwi.nii.gz")
                     ]
                 }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/slices/axial.nii.gz")
+                    ]
+                }
+                input[0] = ch_dwi
+                    .join(ch_mask)
                 """
             }
         }
diff --git a/modules/nf-scil/denoising/mppca/tests/main.nf.test.snap b/modules/nf-scil/denoising/mppca/tests/main.nf.test.snap
index c599bfe7..ab3c336d 100644
--- a/modules/nf-scil/denoising/mppca/tests/main.nf.test.snap
+++ b/modules/nf-scil/denoising/mppca/tests/main.nf.test.snap
@@ -5,33 +5,31 @@
                 "0": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596"
+                        "test_dwi_denoised.nii.gz:md5,697aa941c0cb71fe1865662da5b727fa"
                     ]
                 ],
                 "1": [
-                    "versions.yml:md5,fb589ae27eb3edb1cd1a50b0e13d2714"
+                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
                 ],
                 "image": [
                     [
                         {
-                            "id": "test",
-                            "single_end": false
+                            "id": "test"
                         },
-                        "test_dwi_denoised.nii.gz:md5,c949b91d96513cba506975c271e53596"
+                        "test_dwi_denoised.nii.gz:md5,697aa941c0cb71fe1865662da5b727fa"
                     ]
                 ],
                 "versions": [
-                    "versions.yml:md5,fb589ae27eb3edb1cd1a50b0e13d2714"
+                    "versions.yml:md5,c9915fbc1956d7f54bee0748f1ddf920"
                 ]
             }
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-04-25T11:07:06.152814"
+        "timestamp": "2024-08-05T15:17:51.718413"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-scil/denoising/mppca/tests/nextflow.config b/modules/nf-scil/denoising/mppca/tests/nextflow.config
index a6361aa8..7a19d537 100644
--- a/modules/nf-scil/denoising/mppca/tests/nextflow.config
+++ b/modules/nf-scil/denoising/mppca/tests/nextflow.config
@@ -3,4 +3,5 @@ process {
         publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
         ext.extent = 3
     }
+    cpus = 1
 }
diff --git a/poetry.lock b/poetry.lock
index 89c795f9..67050f3b 100755
--- a/poetry.lock
+++ b/poetry.lock
@@ -1,14 +1,14 @@
 # This file is automatically @generated by Poetry 1.8.3 and should not be changed by hand.
 
 [[package]]
-name = "alabaster"
-version = "0.7.16"
-description = "A light, configurable Sphinx theme"
+name = "annotated-types"
+version = "0.7.0"
+description = "Reusable constraint types to use with typing.Annotated"
 optional = false
-python-versions = ">=3.9"
+python-versions = ">=3.8"
 files = [
-    {file = "alabaster-0.7.16-py3-none-any.whl", hash = "sha256:b46733c07dce03ae4e150330b975c75737fa60f0a7c591b6c8bf4928a28e2c92"},
-    {file = "alabaster-0.7.16.tar.gz", hash = "sha256:75a8b99c28a5dad50dd7f8ccdd447a121ddb3892da9e53d1ca5cca3106d58d65"},
+    {file = "annotated_types-0.7.0-py3-none-any.whl", hash = "sha256:1f02e8b43a8fbbc3f3e0d4f0f4bfc8131bcb4eebe8849b8e5c773f3a1c582a53"},
+    {file = "annotated_types-0.7.0.tar.gz", hash = "sha256:aff07c09a53a08bc8cfccb9c85b05f1aa9a2a6f23728d790723543408344ce89"},
 ]
 
 [[package]]
@@ -27,66 +27,52 @@ ubiquerg = ">=0.2.1"
 
 [[package]]
 name = "attrs"
-version = "23.2.0"
+version = "24.1.0"
 description = "Classes Without Boilerplate"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "attrs-23.2.0-py3-none-any.whl", hash = "sha256:99b87a485a5820b23b879f04c2305b44b951b502fd64be915879d77a7e8fc6f1"},
-    {file = "attrs-23.2.0.tar.gz", hash = "sha256:935dc3b529c262f6cf76e50877d35a4bd3c1de194fd41f47a2b7ae8f19971f30"},
+    {file = "attrs-24.1.0-py3-none-any.whl", hash = "sha256:377b47448cb61fea38533f671fba0d0f8a96fd58facd4dc518e3dac9dbea0905"},
+    {file = "attrs-24.1.0.tar.gz", hash = "sha256:adbdec84af72d38be7628e353a09b6a6790d15cd71819f6e9d7b0faa8a125745"},
 ]
 
 [package.extras]
-cov = ["attrs[tests]", "coverage[toml] (>=5.3)"]
-dev = ["attrs[tests]", "pre-commit"]
-docs = ["furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier", "zope-interface"]
-tests = ["attrs[tests-no-zope]", "zope-interface"]
-tests-mypy = ["mypy (>=1.6)", "pytest-mypy-plugins"]
-tests-no-zope = ["attrs[tests-mypy]", "cloudpickle", "hypothesis", "pympler", "pytest (>=4.3.0)", "pytest-xdist[psutil]"]
-
-[[package]]
-name = "babel"
-version = "2.15.0"
-description = "Internationalization utilities"
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "Babel-2.15.0-py3-none-any.whl", hash = "sha256:08706bdad8d0a3413266ab61bd6c34d0c28d6e1e7badf40a2cebe67644e2e1fb"},
-    {file = "babel-2.15.0.tar.gz", hash = "sha256:8daf0e265d05768bc6c7a314cf1321e9a123afc328cc635c18622a2f30a04413"},
-]
-
-[package.extras]
-dev = ["freezegun (>=1.0,<2.0)", "pytest (>=6.0)", "pytest-cov"]
+benchmark = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-codspeed", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+cov = ["cloudpickle", "coverage[toml] (>=5.3)", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+dev = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pre-commit", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+docs = ["cogapp", "furo", "myst-parser", "sphinx", "sphinx-notfound-page", "sphinxcontrib-towncrier", "towncrier (<24.7)"]
+tests = ["cloudpickle", "hypothesis", "mypy (>=1.11.1)", "pympler", "pytest (>=4.3.0)", "pytest-mypy-plugins", "pytest-xdist[psutil]"]
+tests-mypy = ["mypy (>=1.11.1)", "pytest-mypy-plugins"]
 
 [[package]]
 name = "black"
-version = "24.4.2"
+version = "24.8.0"
 description = "The uncompromising code formatter."
 optional = false
 python-versions = ">=3.8"
 files = [
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-    {file = "black-24.4.2-cp310-cp310-macosx_11_0_arm64.whl", hash = "sha256:8e537d281831ad0e71007dcdcbe50a71470b978c453fa41ce77186bbe0ed6021"},
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 ]
 
 [package.dependencies]
@@ -131,13 +117,13 @@ ujson = ["ujson (>=5.7.0)"]
 
 [[package]]
 name = "certifi"
-version = "2024.2.2"
+version = "2024.7.4"
 description = "Python package for providing Mozilla's CA Bundle."
 optional = false
 python-versions = ">=3.6"
 files = [
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 ]
 
 [[package]]
@@ -340,71 +326,21 @@ files = [
 ]
 
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-name = "coverage"
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-description = "Code coverage measurement for Python"
+name = "coloredlogs"
+version = "15.0.1"
+description = "Colored terminal output for Python's logging module"
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
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+    {file = "coloredlogs-15.0.1-py2.py3-none-any.whl", hash = "sha256:612ee75c546f53e92e70049c9dbfcc18c935a2b9a53b66085ce9ef6a6e5c0934"},
+    {file = "coloredlogs-15.0.1.tar.gz", hash = "sha256:7c991aa71a4577af2f82600d8f8f3a89f936baeaf9b50a9c197da014e5bf16b0"},
 ]
 
 [package.dependencies]
-tomli = {version = "*", optional = true, markers = "python_full_version <= \"3.11.0a6\" and extra == \"toml\""}
+humanfriendly = ">=9.1"
 
 [package.extras]
-toml = ["tomli"]
+cron = ["capturer (>=2.4)"]
 
 [[package]]
 name = "distlib"
@@ -417,17 +353,6 @@ files = [
     {file = "distlib-0.3.8.tar.gz", hash = "sha256:1530ea13e350031b6312d8580ddb6b27a104275a31106523b8f123787f494f64"},
 ]
 
-[[package]]
-name = "docutils"
-version = "0.20.1"
-description = "Docutils -- Python Documentation Utilities"
-optional = false
-python-versions = ">=3.7"
-files = [
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-]
-
 [[package]]
 name = "eido"
 version = "0.2.2"
@@ -448,13 +373,13 @@ ubiquerg = ">=0.5.2"
 
 [[package]]
 name = "exceptiongroup"
-version = "1.2.1"
+version = "1.2.2"
 description = "Backport of PEP 654 (exception groups)"
 optional = false
 python-versions = ">=3.7"
 files = [
-    {file = "exceptiongroup-1.2.1-py3-none-any.whl", hash = "sha256:5258b9ed329c5bbdd31a309f53cbfb0b155341807f6ff7606a1e801a891b29ad"},
-    {file = "exceptiongroup-1.2.1.tar.gz", hash = "sha256:a4785e48b045528f5bfe627b6ad554ff32def154f42372786903b7abcfe1aa16"},
+    {file = "exceptiongroup-1.2.2-py3-none-any.whl", hash = "sha256:3111b9d131c238bec2f8f516e123e14ba243563fb135d3fe885990585aa7795b"},
+    {file = "exceptiongroup-1.2.2.tar.gz", hash = "sha256:47c2edf7c6738fafb49fd34290706d1a1a2f4d1c6df275526b62cbb4aa5393cc"},
 ]
 
 [package.extras]
@@ -462,18 +387,18 @@ test = ["pytest (>=6)"]
 
 [[package]]
 name = "filelock"
-version = "3.14.0"
+version = "3.15.4"
 description = "A platform independent file lock."
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "filelock-3.14.0-py3-none-any.whl", hash = "sha256:43339835842f110ca7ae60f1e1c160714c5a6afd15a2873419ab185334975c0f"},
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+    {file = "filelock-3.15.4-py3-none-any.whl", hash = "sha256:6ca1fffae96225dab4c6eaf1c4f4f28cd2568d3ec2a44e15a08520504de468e7"},
+    {file = "filelock-3.15.4.tar.gz", hash = "sha256:2207938cbc1844345cb01a5a95524dae30f0ce089eba5b00378295a17e3e90cb"},
 ]
 
 [package.extras]
 docs = ["furo (>=2023.9.10)", "sphinx (>=7.2.6)", "sphinx-autodoc-typehints (>=1.25.2)"]
-testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)"]
+testing = ["covdefaults (>=2.3)", "coverage (>=7.3.2)", "diff-cover (>=8.0.1)", "pytest (>=7.4.3)", "pytest-asyncio (>=0.21)", "pytest-cov (>=4.1)", "pytest-mock (>=3.12)", "pytest-timeout (>=2.2)", "virtualenv (>=20.26.2)"]
 typing = ["typing-extensions (>=4.8)"]
 
 [[package]]
@@ -489,13 +414,12 @@ files = [
 
 [[package]]
 name = "future"
-version = "1.0.0"
+version = "0.18.3"
 description = "Clean single-source support for Python 3 and 2"
 optional = false
 python-versions = ">=2.6, !=3.0.*, !=3.1.*, !=3.2.*"
 files = [
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+    {file = "future-0.18.3.tar.gz", hash = "sha256:34a17436ed1e96697a86f9de3d15a3b0be01d8bc8de9c1dffd59fb8234ed5307"},
 ]
 
 [[package]]
@@ -530,15 +454,29 @@ gitdb = ">=4.0.1,<5"
 doc = ["sphinx (==4.3.2)", "sphinx-autodoc-typehints", "sphinx-rtd-theme", "sphinxcontrib-applehelp (>=1.0.2,<=1.0.4)", "sphinxcontrib-devhelp (==1.0.2)", "sphinxcontrib-htmlhelp (>=2.0.0,<=2.0.1)", "sphinxcontrib-qthelp (==1.0.3)", "sphinxcontrib-serializinghtml (==1.1.5)"]
 test = ["coverage[toml]", "ddt (>=1.1.1,!=1.4.3)", "mock", "mypy", "pre-commit", "pytest (>=7.3.1)", "pytest-cov", "pytest-instafail", "pytest-mock", "pytest-sugar", "typing-extensions"]
 
+[[package]]
+name = "humanfriendly"
+version = "10.0"
+description = "Human friendly output for text interfaces using Python"
+optional = false
+python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, !=3.4.*"
+files = [
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+]
+
+[package.dependencies]
+pyreadline3 = {version = "*", markers = "sys_platform == \"win32\" and python_version >= \"3.8\""}
+
 [[package]]
 name = "identify"
-version = "2.5.36"
+version = "2.6.0"
 description = "File identification library for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "identify-2.5.36-py2.py3-none-any.whl", hash = "sha256:37d93f380f4de590500d9dba7db359d0d3da95ffe7f9de1753faa159e71e7dfa"},
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 ]
 
 [package.extras]
@@ -555,35 +493,24 @@ files = [
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-description = "Getting image size from png/jpeg/jpeg2000/gif file"
-optional = false
-python-versions = ">=2.7, !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*"
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-]
-
 [[package]]
 name = "importlib-metadata"
-version = "7.1.0"
+version = "8.2.0"
 description = "Read metadata from Python packages"
 optional = false
 python-versions = ">=3.8"
 files = [
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 [package.dependencies]
 zipp = ">=0.5"
 
 [package.extras]
-docs = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
+doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"]
 perf = ["ipython"]
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+test = ["flufl.flake8", "importlib-resources (>=1.3)", "jaraco.test (>=5.4)", "packaging", "pyfakefs", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-mypy", "pytest-perf (>=0.9.2)", "pytest-ruff (>=0.2.1)"]
 
 [[package]]
 name = "iniconfig"
@@ -681,13 +608,13 @@ i18n = ["Babel (>=2.7)"]
 
 [[package]]
 name = "jsonschema"
-version = "4.22.0"
+version = "4.23.0"
 description = "An implementation of JSON Schema validation for Python"
 optional = false
 python-versions = ">=3.8"
 files = [
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 ]
 
 [package.dependencies]
@@ -698,7 +625,7 @@ rpds-py = ">=0.7.1"
 
 [package.extras]
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+format-nongpl = ["fqdn", "idna", "isoduration", "jsonpointer (>1.13)", "rfc3339-validator", "rfc3986-validator (>0.1.0)", "uri-template", "webcolors (>=24.6.0)"]
 
 [[package]]
 name = "jsonschema-specifications"
@@ -902,32 +829,6 @@ files = [
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 ]
 
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-version = "2.0.0"
-description = "An extended [CommonMark](https://spec.commonmark.org/) compliant parser,"
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-python-versions = ">=3.8"
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-mdit-py-plugins = ">=0.4,<1.0"
-pyyaml = "*"
-sphinx = ">=6,<8"
-
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-
 [[package]]
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 version = "2.14.1"
@@ -963,92 +864,52 @@ rich-click = ">=1.6.1"
 tabulate = "*"
 trogon = "*"
 
-[[package]]
-name = "nibabel"
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-all = ["nibabel[dicomfs,minc2,spm,zstd]"]
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-dicom = ["pydicom (>=1.0.0)"]
-dicomfs = ["nibabel[dicom]", "pillow"]
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-typing = ["tox"]
-zstd = ["pyzstd (>=0.14.3)"]
-
 [[package]]
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 description = "Node.js virtual environment builder"
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-python-versions = ">=2.7,!=3.0.*,!=3.1.*,!=3.2.*,!=3.3.*,!=3.4.*,!=3.5.*,!=3.6.*"
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 tzdata = ">=2022.7"
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 [package.dependencies]
 colorama = "*"
 
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 [package.extras]
@@ -1305,13 +1182,13 @@ plot = ["matplotlib", "scipy", "seaborn"]
 
 [[package]]
 name = "pipestat"
-version = "0.9.1"
+version = "0.10.0"
 description = "A pipeline results reporter"
 optional = false
 python-versions = "*"
 files = [
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 ]
 
 [package.dependencies]
@@ -1330,19 +1207,18 @@ pipestatreader = ["fastapi", "uvicorn"]
 
 [[package]]
 name = "platformdirs"
-version = "4.2.2"
-description = "A small Python package for determining appropriate platform-specific dirs, e.g. a `user data dir`."
+version = "3.11.0"
+description = "A small Python package for determining appropriate platform-specific dirs, e.g. a \"user data dir\"."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7"
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-type = ["mypy (>=1.8)"]
+docs = ["furo (>=2023.7.26)", "proselint (>=0.13)", "sphinx (>=7.1.1)", "sphinx-autodoc-typehints (>=1.24)"]
+test = ["appdirs (==1.4.4)", "covdefaults (>=2.3)", "pytest (>=7.4)", "pytest-cov (>=4.1)", "pytest-mock (>=3.11.1)"]
 
 [[package]]
 name = "pluggy"
@@ -1361,13 +1237,13 @@ testing = ["pytest", "pytest-benchmark"]
 
 [[package]]
 name = "pre-commit"
-version = "3.7.1"
+version = "3.8.0"
 description = "A framework for managing and maintaining multi-language pre-commit hooks."
 optional = false
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+]
+
+[package.dependencies]
+typing-extensions = ">=4.6.0,<4.7.0 || >4.7.0"
+
 [[package]]
 name = "pyfaidx"
 version = "0.8.1.1"
@@ -1460,58 +1457,38 @@ files = [
 windows-terminal = ["colorama (>=0.4.6)"]
 
 [[package]]
-name = "pytest"
-version = "8.2.1"
-description = "pytest: simple powerful testing with Python"
+name = "pyreadline3"
+version = "3.4.1"
+description = "A python implementation of GNU readline."
 optional = false
-python-versions = ">=3.8"
+python-versions = "*"
 files = [
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 ]
 
-[package.dependencies]
-colorama = {version = "*", markers = "sys_platform == \"win32\""}
-exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
-iniconfig = "*"
-packaging = "*"
-pluggy = ">=1.5,<2.0"
-tomli = {version = ">=1", markers = "python_version < \"3.11\""}
-
-[package.extras]
-dev = ["argcomplete", "attrs (>=19.2)", "hypothesis (>=3.56)", "mock", "pygments (>=2.7.2)", "requests", "setuptools", "xmlschema"]
-
 [[package]]
-name = "pytest-cov"
-version = "4.1.0"
-description = "Pytest plugin for measuring coverage."
+name = "pytest"
+version = "7.2.2"
+description = "pytest: simple powerful testing with Python"
 optional = false
 python-versions = ">=3.7"
 files = [
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 ]
 
 [package.dependencies]
-coverage = {version = ">=5.2.1", extras = ["toml"]}
-pytest = ">=4.6"
+attrs = ">=19.2.0"
+colorama = {version = "*", markers = "sys_platform == \"win32\""}
+exceptiongroup = {version = ">=1.0.0rc8", markers = "python_version < \"3.11\""}
+iniconfig = "*"
+packaging = "*"
+pluggy = ">=0.12,<2.0"
+tomli = {version = ">=1.0.0", markers = "python_version < \"3.11\""}
 
 [package.extras]
-testing = ["fields", "hunter", "process-tests", "pytest-xdist", "six", "virtualenv"]
-
-[[package]]
-name = "pytest-datafiles"
-version = "3.0.0"
-description = "py.test plugin to create a 'tmp_path' containing predefined files/directories."
-optional = false
-python-versions = "*"
-files = [
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-]
-
-[package.dependencies]
-pytest = ">=3.6"
+testing = ["argcomplete", "hypothesis (>=3.56)", "mock", "nose", "pygments (>=2.7.2)", "requests", "xmlschema"]
 
 [[package]]
 name = "pytest-workflow"
@@ -1533,13 +1510,13 @@ zstandard = "*"
 
 [[package]]
 name = "python-dateutil"
-version = "2.9.0.post0"
+version = "2.8.2"
 description = "Extensions to the standard Python datetime module"
 optional = false
 python-versions = "!=3.0.*,!=3.1.*,!=3.2.*,>=2.7"
 files = [
-    {file = "python-dateutil-2.9.0.post0.tar.gz", hash = "sha256:37dd54208da7e1cd875388217d5e00ebd4179249f90fb72437e91a35459a0ad3"},
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+    {file = "python-dateutil-2.8.2.tar.gz", hash = "sha256:0123cacc1627ae19ddf3c27a5de5bd67ee4586fbdd6440d9748f8abb483d3e86"},
+    {file = "python_dateutil-2.8.2-py2.py3-none-any.whl", hash = "sha256:961d03dc3453ebbc59dbdea9e4e11c5651520a876d0f4db161e8674aae935da9"},
 ]
 
 [package.dependencies]
@@ -1547,13 +1524,13 @@ six = ">=1.5"
 
 [[package]]
 name = "pytz"
-version = "2024.1"
+version = "2022.6"
 description = "World timezone definitions, modern and historical"
 optional = false
 python-versions = "*"
 files = [
-    {file = "pytz-2024.1-py2.py3-none-any.whl", hash = "sha256:328171f4e3623139da4983451950b28e95ac706e13f3f2630a879749e7a8b319"},
-    {file = "pytz-2024.1.tar.gz", hash = "sha256:2a29735ea9c18baf14b448846bde5a48030ed267578472d8955cd0e7443a9812"},
+    {file = "pytz-2022.6-py2.py3-none-any.whl", hash = "sha256:222439474e9c98fced559f1709d89e6c9cbf8d79c794ff3eb9f8800064291427"},
+    {file = "pytz-2022.6.tar.gz", hash = "sha256:e89512406b793ca39f5971bc999cc538ce125c0e51c27941bef4568b460095e2"},
 ]
 
 [[package]]
@@ -1689,20 +1666,20 @@ yacman = ">=0.8.3"
 
 [[package]]
 name = "requests"
-version = "2.32.1"
+version = "2.28.2"
 description = "Python HTTP for Humans."
 optional = false
-python-versions = ">=3.8"
+python-versions = ">=3.7, <4"
 files = [
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-    {file = "requests-2.32.1.tar.gz", hash = "sha256:eb97e87e64c79e64e5b8ac75cee9dd1f97f49e289b083ee6be96268930725685"},
+    {file = "requests-2.28.2-py3-none-any.whl", hash = "sha256:64299f4909223da747622c030b781c0d7811e359c37124b4bd368fb8c6518baa"},
+    {file = "requests-2.28.2.tar.gz", hash = "sha256:98b1b2782e3c6c4904938b84c0eb932721069dfdb9134313beff7c83c2df24bf"},
 ]
 
 [package.dependencies]
 certifi = ">=2017.4.17"
 charset-normalizer = ">=2,<4"
 idna = ">=2.5,<4"
-urllib3 = ">=1.21.1,<3"
+urllib3 = ">=1.21.1,<1.27"
 
 [package.extras]
 socks = ["PySocks (>=1.5.6,!=1.5.7)"]
@@ -1710,13 +1687,13 @@ use-chardet-on-py3 = ["chardet (>=3.0.2,<6)"]
 
 [[package]]
 name = "requests-cache"
-version = "1.2.0"
+version = "1.2.1"
 description = "A persistent cache for python requests"
 optional = false
 python-versions = ">=3.8"
 files = [
-    {file = "requests_cache-1.2.0-py3-none-any.whl", hash = "sha256:490324301bf0cb924ff4e6324bd2613453e7e1f847353928b08adb0fdfb7f722"},
-    {file = "requests_cache-1.2.0.tar.gz", hash = "sha256:db1c709ca343cc1cd5b6c8b1a5387298eceed02306a6040760db538c885e3838"},
+    {file = "requests_cache-1.2.1-py3-none-any.whl", hash = "sha256:1285151cddf5331067baa82598afe2d47c7495a1334bfe7a7d329b43e9fd3603"},
+    {file = "requests_cache-1.2.1.tar.gz", hash = "sha256:68abc986fdc5b8d0911318fbb5f7c80eebcd4d01bfacc6685ecf8876052511d1"},
 ]
 
 [package.dependencies]
@@ -1738,25 +1715,6 @@ redis = ["redis (>=3)"]
 security = ["itsdangerous (>=2.0)"]
 yaml = ["pyyaml (>=6.0.1)"]
 
-[[package]]
-name = "responses"
-version = "0.24.1"
-description = "A utility library for mocking out the `requests` Python library."
-optional = false
-python-versions = ">=3.8"
-files = [
-    {file = "responses-0.24.1-py3-none-any.whl", hash = "sha256:a2b43f4c08bfb9c9bd242568328c65a34b318741d3fab884ac843c5ceeb543f9"},
-    {file = "responses-0.24.1.tar.gz", hash = "sha256:b127c6ca3f8df0eb9cc82fd93109a3007a86acb24871834c47b77765152ecf8c"},
-]
-
-[package.dependencies]
-pyyaml = "*"
-requests = ">=2.30.0,<3.0"
-urllib3 = ">=1.25.10,<3.0"
-
-[package.extras]
-tests = ["coverage (>=6.0.0)", "flake8", "mypy", "pytest (>=7.0.0)", "pytest-asyncio", "pytest-cov", "pytest-httpserver", "tomli", "tomli-w", "types-PyYAML", "types-requests"]
-
 [[package]]
 name = "rich"
 version = "13.7.1"
@@ -1777,13 +1735,13 @@ jupyter = ["ipywidgets (>=7.5.1,<9)"]
 
 [[package]]
 name = "rich-click"
-version = "1.8.2"
+version = "1.8.3"
 description = "Format click help output nicely with rich"
 optional = false
 python-versions = ">=3.7"
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 [package.dependencies]
@@ -1797,126 +1755,142 @@ docs = ["markdown-include", "mkdocs", "mkdocs-glightbox", "mkdocs-material-exten
 
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 [package.dependencies]
@@ -2193,15 +1993,32 @@ files = [
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 textual = ">=0.26.0"
 
+[[package]]
+name = "typer"
+version = "0.12.3"
+description = "Typer, build great CLIs. Easy to code. Based on Python type hints."
+optional = false
+python-versions = ">=3.7"
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+rich = ">=10.11.0"
+shellingham = ">=1.3.0"
+typing-extensions = ">=3.7.4.3"
+
 [[package]]
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 python-versions = ">=3.8"
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 [[package]]
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 [[package]]
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 description = "HTTP library with thread-safe connection pooling, file post, and more."
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 [package.dependencies]
@@ -2304,13 +2120,13 @@ files = [
 
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 description = "Open compressed files transparently"
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 python-versions = ">=3.8"
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@@ -2341,18 +2157,18 @@ ubiquerg = ">=0.7.0"
 
 [[package]]
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 ]
 
 [package.dependencies]
@@ -2469,5 +2336,5 @@ cffi = ["cffi (>=1.11)"]
 
 [metadata]
 lock-version = "2.0"
-python-versions = "<3.13,>=3.9"
-content-hash = "2b8a6c5d186235af71e0da40a5dadcf51d54098414aa245deaa1d6a2ac351bba"
+python-versions = "<3.11,>=3.9"
+content-hash = "86ff61aa15873147e59b28a6ff0b1ac405796dde631e28216829299332fdfa26"
diff --git a/poetry.toml b/poetry.toml
index ab1033bd..fc4e4cb9 100755
--- a/poetry.toml
+++ b/poetry.toml
@@ -1,2 +1,5 @@
 [virtualenvs]
 in-project = true
+
+[virtualenvs.options]
+system-site-packages = true
diff --git a/pyproject.toml b/pyproject.toml
index 94c2513e..376cbd03 100755
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -24,17 +24,7 @@ repository = "https://github.com/scilus/nf-scil.git"
 
 [tool.poetry.dependencies]
 
-python = "<3.13,>=3.9"
+python = "<3.11,>=3.9"
 nf-core = "~2.14.1"
-nibabel = "^5.1.0"
-numpy = "^1.24"
-requests = "^2.28"
 black = "^24.1.1"
 isort = "^5.13.2"
-myst-parser = "^2.0.0"
-pytest-cov = "^4.1.0"
-pytest-datafiles = "^3.0.0"
-pytest-workflow = ">=2.0.0"
-responses = "^0.24.1"
-sphinx = "^7.2.6"
-sphinx-rtd-theme = "^2.0.0"
diff --git a/subworkflows/nf-scil/preproc_dwi/main.nf b/subworkflows/nf-scil/preproc_dwi/main.nf
index 7a6b730d..25359161 100644
--- a/subworkflows/nf-scil/preproc_dwi/main.nf
+++ b/subworkflows/nf-scil/preproc_dwi/main.nf
@@ -31,7 +31,10 @@ workflow PREPROC_DWI {
             }
 
         // ** Denoised DWI ** //
-        DENOISE_DWI ( ch_denoise_dwi.dwi )
+        DENOISE_DWI (
+            ch_denoise_dwi.dwi
+                .map{ it + [[]] }
+        )
         ch_versions = ch_versions.mix(DENOISE_DWI.out.versions.first())
 
         if ( ch_rev_dwi )
@@ -42,7 +45,10 @@ workflow PREPROC_DWI {
                     rev_bvs_files: [ meta, bval, bvec ]
                 }
             // ** Denoised reverse DWI ** //
-            DENOISE_REVDWI ( ch_denoise_rev_dwi.rev_dwi )
+            DENOISE_REVDWI (
+                ch_denoise_rev_dwi.rev_dwi
+                    .map{ it + [[]] }
+            )
             ch_versions = ch_versions.mix(DENOISE_REVDWI.out.versions.first())
 
             ch_topup_eddy_rev_dwi = DENOISE_REVDWI.out.image
diff --git a/subworkflows/nf-scil/preproc_dwi/tests/main.nf.test.snap b/subworkflows/nf-scil/preproc_dwi/tests/main.nf.test.snap
index 528a24f2..60fb0c25 100644
--- a/subworkflows/nf-scil/preproc_dwi/tests/main.nf.test.snap
+++ b/subworkflows/nf-scil/preproc_dwi/tests/main.nf.test.snap
@@ -12,15 +12,15 @@
             ],
             [
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
-                "versions.yml:md5,1662ab8cb093ea6d16798a8fa82639e1",
+                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
                 "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
                 "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
                 "versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
-                "versions.yml:md5,977c7cd0a14188f1dfeb0f69a819b79e",
                 "versions.yml:md5,b4c068383da080f871c90828b1de0082",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
                 "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
                 "versions.yml:md5,d3010f785c88ee5946806a8a758e7efb",
+                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
             "test_b0.nii.gz",
@@ -32,10 +32,10 @@
             "test__dwi_corrected.nii.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-10T20:02:02.685487"
+        "timestamp": "2024-08-05T18:15:01.714505"
     },
     "preproc_dwi_rev_b0": {
         "content": [
@@ -50,10 +50,10 @@
             ],
             [
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
+                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
                 "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
                 "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
                 "versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
-                "versions.yml:md5,977c7cd0a14188f1dfeb0f69a819b79e",
                 "versions.yml:md5,b4c068383da080f871c90828b1de0082",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
                 "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
@@ -69,10 +69,10 @@
             "test__dwi_corrected.nii.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-10T19:59:48.024911"
+        "timestamp": "2024-08-05T18:10:40.247701"
     },
     "preproc_dwi_all_options": {
         "content": [
@@ -87,14 +87,14 @@
             ],
             [
                 "versions.yml:md5,0280006ceecc575513278292734ffb27",
-                "versions.yml:md5,1662ab8cb093ea6d16798a8fa82639e1",
+                "versions.yml:md5,3340c4b5e56ca52f7342be3c9044eb47",
                 "versions.yml:md5,4d981a0200b8820dd789f135a9dd320f",
                 "versions.yml:md5,5dce7a8c0b0d6b91ef7826f88c86370e",
                 "versions.yml:md5,962f76092c8795ce5e6d768304e2d230",
-                "versions.yml:md5,977c7cd0a14188f1dfeb0f69a819b79e",
                 "versions.yml:md5,b4c068383da080f871c90828b1de0082",
                 "versions.yml:md5,c15ba5efd24564dba4710b6da8c4b791",
                 "versions.yml:md5,d1ae2ca80502bf88c4b1c4a42fba6ced",
+                "versions.yml:md5,d68fe3399120f84f1add62181708780b",
                 "versions.yml:md5,f041502e22449973d84ac1c618e8ebf9"
             ],
             "test_b0.nii.gz",
@@ -106,9 +106,9 @@
             "test__dwi_corrected.nii.gz"
         ],
         "meta": {
-            "nf-test": "0.8.4",
-            "nextflow": "23.10.1"
+            "nf-test": "0.9.0-rc1",
+            "nextflow": "24.04.4"
         },
-        "timestamp": "2024-05-10T20:04:37.270376"
+        "timestamp": "2024-08-05T18:20:22.568596"
     }
 }
\ No newline at end of file
diff --git a/tests/config/nf-test.config b/tests/config/nf-test.config
index 799e9e34..db1187ea 100644
--- a/tests/config/nf-test.config
+++ b/tests/config/nf-test.config
@@ -33,7 +33,30 @@ params {
         "antsbet.zip": "66850bea7af7c1f3fc4e7d371d12d6e8",
         "freesurfer.zip": "3b876fba6fd77d4962243ac9647bc505",
         "light.zip": "f2a3a8bddf43d1f67a5e8867ce9ebaa2",
-        "heavy.zip": "6f2cd0bbdb162455e71de1c7d3b4eb18"
+        "heavy.zip": "6f2cd0bbdb162455e71de1c7d3b4eb18",
+        "raw_b0.zip": "6e7b8181b3e929f4235a9364aa60656b",
+        "raw_DWIms300-1000-2000-dir8-32-60.zip": "cfa4cb9cc9595a18272fdb0ef3a08ce5",
+        "raw_DWIms300-1000-dir8-32.zip": "29dfaba220a1e921f95e16f811977f36",
+        "raw_DWIms1000-2000-dir32-60.zip": "7fed32798f158ab8118a116fd9a69f52",
+        "raw_DWIss300-dir8.zip": "33e735bf7514159b803f8302f4d97db8",
+        "raw_DWIss1000-dir32.zip": "55246c8f6fe8c04cb8538715cad21c38",
+        "raw_DWIss2000-dir60.zip": "8dc746ccf9eed5f8931265bad379e2e5",
+        "raw_EPI.zip": "631e9781bda5ae482d92bba1c612bbf5",
+        "raw_FLAIR.zip": "67663a38ce23120b1b42d73fa9268d2d",
+        "raw_T1w.zip": "2a4adad9dd05a0fb626cb71945bc11b5",
+        "raw_segmentation.zip": "6aac249229e1e360d1fca90bc4a4bec2",
+        "topup_results.zip": "f83628eac00c9851cb015588909c4ef8",
+        "b0.zip": "fefd7452a61a80f6ceac7352e6231a0d",
+        "DWIms300-1000-2000-dir8-32-60.zip": "6249618893c832dfb4392c72fd7c81cb",
+        "DWIms300-1000-dir8-32.zip": "52e67fa54a2494d2ad5b496d25e6ee99",
+        "DWIms1000-2000-dir32-60.zip": "5db0cc6624da1d5ec99893b08629e45f",
+        "DWIss300-dir8.zip": "ef1335775c9fbf11452c71e01b097282",
+        "DWIss1000-dir32.zip": "c72fd590a3f400278299a068eeffd1d0",
+        "DWIss2000-dir60.zip": "9ad7ccb4e30b39c47f374018db2e6424",
+        "T1w.zip": "10e27bb2ddd4d01be968a93b2166096c",
+        "dti.zip": "ba866c59fc4d984f626691a6b941fc32",
+        "responses.zip": "1a5b862b91c72740bcce0431a1f9254a",
+        "segmentation.zip": "ab51be6d142ad1a8e30ffb964447d010"
     ]
 }