diff --git a/.gitignore b/.gitignore
index 69744f0..4223c1c 100644
--- a/.gitignore
+++ b/.gitignore
@@ -5,4 +5,6 @@
 
 tests/.runs/
 work/
-.nf-test/
\ No newline at end of file
+.nf-test/
+result
+.DS_Store
\ No newline at end of file
diff --git a/assets/multiqc_config.yml b/assets/multiqc_config.yml
new file mode 100644
index 0000000..0ecdba5
--- /dev/null
+++ b/assets/multiqc_config.yml
@@ -0,0 +1,21 @@
+report_comment: >
+  This report has been generated by the nf-neuro tutorial!
+
+report_section_order:
+  dti_qc:
+    order: -1001
+
+custom_data:
+  dti_qc:
+    file_format: "png"
+    section_name: "DTI QC"
+    description: |
+      This section contains QC images for diffusion tensor imaging (DTI) metric
+      maps. Add specifications regarding how to evaluate those images, for example:
+      To assess the quality of the DTI metrics, ensure that FA highlights major white
+      matter tracts with expected high values (e.g., corpus callosum, corticospinal tract, etc.)...
+    plot_type: "image"
+
+sp:
+  dti_qc:
+    fn: "*dti_mqc.png"
\ No newline at end of file
diff --git a/main.nf b/main.nf
index 754faf1..e3aa586 100644
--- a/main.nf
+++ b/main.nf
@@ -1,30 +1,91 @@
 #!/usr/bin/env nextflow
 
-//include { RECONST_DTIMETRICS } from 'modules/nf-neuro/reconst/dtimetrics/main'
+include { PREPROC_T1 } from './subworkflows/nf-neuro/preproc_t1/main'
+include { STATS_METRICSINROI } from './modules/local/stats/metricsinrois/main'
+include { PREPROC_DIFF } from './subworkflows/local/preproc_diff/main'
+include { MULTIQC } from "./modules/nf-core/multiqc/main"
+
 workflow get_data {
     main:
         if ( !params.input ) {
-            log.info "You must provide an input directory containing all files using:"
+            log.info "You must provide an input directory containing all images using:"
             log.info ""
-            log.info "    --input=/path/to/[input]   Input directory containing the file needed"
+            log.info "    --input=/path/to/[input]   Input directory containing your subjects"
             log.info "                        |"
-            log.info "                        └-- Input"
-            log.info "                             └-- participants.*"
+            log.info "                        ├-- S1"
+            log.info "                        |    ├-- *dwi.nii.gz"
+            log.info "                        |    ├-- *dwi.bval"
+            log.info "                        |    ├-- *dwi.bvec"
+            log.info "                        |    └-- *t1.nii.gz"
+            log.info "                        └-- S2"
+            log.info "                             ├-- *dwi.nii.gz"
+            log.info "                             ├-- *bval"
+            log.info "                             ├-- *bvec"
+            log.info "                             └-- *t1.nii.gz"
             log.info ""
             error "Please resubmit your command with the previous file structure."
         }
 
         input = file(params.input)
-        // ** Loading all files. ** //
-        participants_channel = Channel.fromFilePairs("$input/participants.*", flat: true)
-            { "participants_files" }
-
+        // ** Loading DWI files. ** //
+        dwi_channel = Channel.fromFilePairs("$input/**/**/dwi/*dwi.{nii.gz,bval,bvec}", size: 3, flat: true)
+            { it.parent.parent.parent.name + "_" + it.parent.parent.name} // Set the subject filename as subjectID + '_' + session.
+            .map{ sid, bvals, bvecs, dwi -> [ [id: sid], dwi, bvals, bvecs ] } // Reordering the inputs.
+        // ** Loading T1 file. ** //
+        t1_channel = Channel.fromFilePairs("$input/**/**/anat/*T1w.nii.gz", size: 1, flat: true)
+            { it.parent.parent.parent.name + "_" + it.parent.parent.name } // Set the subject filename as subjectID + '_' + session.
+            .map{ sid, t1 -> [ [id: sid], t1 ] }
     emit:
-        participants = participants_channel
+        dwi = dwi_channel
+        anat = t1_channel
 }
 
 workflow {
-    // ** Now call your input workflow to fetch your files ** //
-    data = get_data()
-    data.participants.view()
+    ch_multiqc_files = Channel.empty()
+
+    inputs = get_data()
+
+    //Processing DWI
+    PREPROC_DIFF( inputs.dwi )
+    ch_multiqc_files = ch_multiqc_files.mix(PREPROC_DIFF.out.mqc)
+
+    // Preprocessing T1 images
+    //inputs.anat.view()
+
+    PREPROC_T1(
+        inputs.anat,
+        Channel.empty(),
+        Channel.empty(),
+        Channel.empty(),
+        Channel.empty(),
+        Channel.empty(),
+        Channel.empty()
+    )
+
+    // Extract FA value
+     input_extract_metric = PREPROC_T1.out.image_bet
+             .join(PREPROC_DIFF.out.fa)
+             .map{ it }
+
+    STATS_METRICSINROI( input_extract_metric )
+
+    ch_multiqc_files = ch_multiqc_files
+        .groupTuple()
+        .map { meta, files_list ->
+            def files = files_list.flatten().findAll { it != null }
+            return tuple(meta, files)
+        }
+            
+    ch_multiqc_config = Channel.fromPath("$projectDir/assets/multiqc_config.yml", checkIfExists: true)
+
+    // MultiQC
+    MULTIQC(
+        ch_multiqc_files,
+        [],
+        ch_multiqc_config.toList(),
+        [],
+        [],
+        [],
+        []
+    )
 }
\ No newline at end of file
diff --git a/modules.json b/modules.json
index 7dd2540..9886e83 100644
--- a/modules.json
+++ b/modules.json
@@ -2,12 +2,58 @@
   "name": "",
   "homePage": "",
   "repos": {
+    "https://github.com/nf-core/modules.git": {
+      "modules": {
+        "nf-core": {
+          "multiqc": {
+            "branch": "master",
+            "git_sha": "81880787133db07d9b4c1febd152c090eb8325dc",
+            "installed_by": ["modules"]
+          }
+        }
+      }
+    },
     "https://github.com/scilus/nf-neuro.git": {
       "modules": {
         "nf-neuro": {
+          "betcrop/antsbet": {
+            "branch": "main",
+            "git_sha": "b8949dd284432bbe1399dbc3f54cdf9191855f8e",
+            "installed_by": ["preproc_t1"]
+          },
+          "betcrop/synthbet": {
+            "branch": "main",
+            "git_sha": "dca20370d97a69c6a91c80843f417206212568e6",
+            "installed_by": ["preproc_t1"]
+          },
+          "denoising/mppca": {
+            "branch": "main",
+            "git_sha": "2e222d18c89e5547a6bf5c0c74673baeb63bcd52",
+            "installed_by": ["modules"]
+          },
+          "denoising/nlmeans": {
+            "branch": "main",
+            "git_sha": "261a7e0606645eeaf863e401cb9fc99c130b3a19",
+            "installed_by": ["preproc_t1"]
+          },
+          "image/cropvolume": {
+            "branch": "main",
+            "git_sha": "3e2e971f5bdaafcd5f72cb9c69f9d0b2a6f20de3",
+            "installed_by": ["preproc_t1"]
+          },
+          "image/resample": {
+            "branch": "main",
+            "git_sha": "36e010a236a0bd86334ab99b0cac4f7c4ff51532",
+            "installed_by": ["preproc_t1"]
+          },
+          "preproc/n4": {
+            "branch": "main",
+            "git_sha": "18273a2cef9ffdaf7088e305b9c4ebf4dd439079",
+            "installed_by": ["preproc_t1"]
+          },
           "reconst/dtimetrics": {
             "branch": "main",
-            "git_sha": "452075a707a9769b0509fc33a1051e8ba80799bf",
+            "git_sha": "47e91ecc151180b81de0d4945c892bd616a6ad03",
             "installed_by": ["modules"]
           }
         }
@@ -18,6 +64,11 @@
             "branch": "main",
             "git_sha": "a79cb5c9645269db389c563f674b17c5e900a50b",
             "installed_by": ["subworkflows"]
+          },
+          "preproc_t1": {
+            "branch": "main",
+            "git_sha": "84317cd68567fa8651c120bd19028177f90d41ae",
+            "installed_by": ["subworkflows"]
           }
         }
       }
diff --git a/modules/local/stats/metricsinrois/main.nf b/modules/local/stats/metricsinrois/main.nf
new file mode 100644
index 0000000..62c4a8b
--- /dev/null
+++ b/modules/local/stats/metricsinrois/main.nf
@@ -0,0 +1,46 @@
+process STATS_METRICSINROI {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_latest.sif':
+        'scilus/scilus:latest' }"
+
+    input:
+    tuple val(meta), path(t1), path(metrics)
+
+    output:
+    tuple val(meta), path("*.json")                         , emit: stats
+    tuple val(meta), path("*mask_wm.nii.gz")                , emit: wm_mask
+    tuple val(meta), path("*mask_gm.nii.gz")                , emit: gm_mask
+    tuple val(meta), path("*mask_csf.nii.gz")               , emit: csf_mask
+    tuple val(meta), path("*map_wm.nii.gz")                 , emit: wm_map
+    tuple val(meta), path("*map_gm.nii.gz")                 , emit: gm_map
+    tuple val(meta), path("*map_csf.nii.gz")                , emit: csf_map
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_stats" : "stats"
+    def bin = task.ext.bin ? "--bin " : ""
+    def normalize_weights = task.ext.normalize_weights ? "--normalize_weights " : ""
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    fast -t 1 -n 3\
+        -H 0.1 -I 4 -l 20.0 -g -o t1.nii.gz $t1
+    scil_volume_math.py convert t1_seg_2.nii.gz ${prefix}__mask_wm.nii.gz --data_type uint8
+    scil_volume_math.py convert t1_seg_1.nii.gz ${prefix}__mask_gm.nii.gz --data_type uint8
+    scil_volume_math.py convert t1_seg_0.nii.gz ${prefix}__mask_csf.nii.gz --data_type uint8
+    mv t1_pve_2.nii.gz ${prefix}__map_wm.nii.gz
+    mv t1_pve_1.nii.gz ${prefix}__map_gm.nii.gz
+    mv t1_pve_0.nii.gz ${prefix}__map_csf.nii.gz
+
+    scil_volume_stats_in_ROI.py ${prefix}__mask*.nii.gz  \
+        --metrics $metrics \
+        --sort_keys \
+        $bin $normalize_weights > ${prefix}__${suffix}.json
+
+    """
+}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/environment.yml b/modules/nf-core/multiqc/environment.yml
new file mode 100644
index 0000000..c3b3413
--- /dev/null
+++ b/modules/nf-core/multiqc/environment.yml
@@ -0,0 +1,7 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/nf-core/modules/master/modules/environment-schema.json
+channels:
+  - conda-forge
+  - bioconda
+dependencies:
+  - bioconda::multiqc=1.27
diff --git a/modules/nf-core/multiqc/main.nf b/modules/nf-core/multiqc/main.nf
new file mode 100644
index 0000000..fa35959
--- /dev/null
+++ b/modules/nf-core/multiqc/main.nf
@@ -0,0 +1,63 @@
+process MULTIQC {
+    tag "$meta.id"
+    label 'process_single'
+
+    conda "${moduleDir}/environment.yml"
+    container "${ 'multiqc/multiqc:v1.27.1' }"
+
+    input:
+    tuple val(meta), path(qc_images) // Added input with subject meta field.
+    path  multiqc_files
+    path(multiqc_config)
+    path(extra_multiqc_config)
+    path(multiqc_logo)
+    path(replace_names)
+    path(sample_names)
+
+    output:
+    path "*multiqc_report.html", emit: report
+    path "*_data"              , emit: data
+    path "*_plots"             , optional:true, emit: plots
+    path "versions.yml"        , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = "--filename ${meta.id}_multiqc_report"
+    def config = multiqc_config ? "--config $multiqc_config" : ''
+    def extra_config = extra_multiqc_config ? "--config $extra_multiqc_config" : ''
+    def logo = multiqc_logo ? "--cl-config 'custom_logo: \"${multiqc_logo}\"'" : ''
+    def replace = replace_names ? "--replace-names ${replace_names}" : ''
+    def samples = sample_names ? "--sample-names ${sample_names}" : ''
+    """
+    multiqc \\
+        --force \\
+        $args \\
+        $config \\
+        $prefix \\
+        $extra_config \\
+        $logo \\
+        $replace \\
+        $samples \\
+        .
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    mkdir multiqc_data
+    mkdir multiqc_plots
+    touch multiqc_report.html
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        multiqc: \$( multiqc --version | sed -e "s/multiqc, version //g" )
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-core/multiqc/meta.yml b/modules/nf-core/multiqc/meta.yml
new file mode 100644
index 0000000..b16c187
--- /dev/null
+++ b/modules/nf-core/multiqc/meta.yml
@@ -0,0 +1,78 @@
+name: multiqc
+description: Aggregate results from bioinformatics analyses across many samples into
+  a single report
+keywords:
+  - QC
+  - bioinformatics tools
+  - Beautiful stand-alone HTML report
+tools:
+  - multiqc:
+      description: |
+        MultiQC searches a given directory for analysis logs and compiles a HTML report.
+        It's a general use tool, perfect for summarising the output from numerous bioinformatics tools.
+      homepage: https://multiqc.info/
+      documentation: https://multiqc.info/docs/
+      licence: ["GPL-3.0-or-later"]
+      identifier: biotools:multiqc
+input:
+  - - multiqc_files:
+        type: file
+        description: |
+          List of reports / files recognised by MultiQC, for example the html and zip output of FastQC
+  - - multiqc_config:
+        type: file
+        description: Optional config yml for MultiQC
+        pattern: "*.{yml,yaml}"
+  - - extra_multiqc_config:
+        type: file
+        description: Second optional config yml for MultiQC. Will override common sections
+          in multiqc_config.
+        pattern: "*.{yml,yaml}"
+  - - multiqc_logo:
+        type: file
+        description: Optional logo file for MultiQC
+        pattern: "*.{png}"
+  - - replace_names:
+        type: file
+        description: |
+          Optional two-column sample renaming file. First column a set of
+          patterns, second column a set of corresponding replacements. Passed via
+          MultiQC's `--replace-names` option.
+        pattern: "*.{tsv}"
+  - - sample_names:
+        type: file
+        description: |
+          Optional TSV file with headers, passed to the MultiQC --sample_names
+          argument.
+        pattern: "*.{tsv}"
+output:
+  - report:
+      - "*multiqc_report.html":
+          type: file
+          description: MultiQC report file
+          pattern: "multiqc_report.html"
+  - data:
+      - "*_data":
+          type: directory
+          description: MultiQC data dir
+          pattern: "multiqc_data"
+  - plots:
+      - "*_plots":
+          type: file
+          description: Plots created by MultiQC
+          pattern: "*_data"
+  - versions:
+      - versions.yml:
+          type: file
+          description: File containing software versions
+          pattern: "versions.yml"
+authors:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
+maintainers:
+  - "@abhi18av"
+  - "@bunop"
+  - "@drpatelh"
+  - "@jfy133"
diff --git a/modules/nf-core/multiqc/tests/main.nf.test b/modules/nf-core/multiqc/tests/main.nf.test
new file mode 100644
index 0000000..33316a7
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test
@@ -0,0 +1,92 @@
+nextflow_process {
+
+    name "Test Process MULTIQC"
+    script "../main.nf"
+    process "MULTIQC"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "multiqc"
+
+    config "./nextflow.config"
+
+    test("sarscov2 single-end [fastqc]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_single") }
+            )
+        }
+
+    }
+
+    test("sarscov2 single-end [fastqc] [config]") {
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = Channel.of(file("https://github.com/nf-core/tools/raw/dev/nf_core/pipeline-template/assets/multiqc_config.yml", checkIfExists: true))
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert process.out.report[0] ==~ ".*/multiqc_report.html" },
+                { assert process.out.data[0] ==~ ".*/multiqc_data" },
+                { assert snapshot(process.out.versions).match("multiqc_versions_config") }
+            )
+        }
+    }
+
+    test("sarscov2 single-end [fastqc] - stub") {
+
+        options "-stub"
+
+        when {
+            process {
+                """
+                input[0] = Channel.of(file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fastqc/test_fastqc.zip', checkIfExists: true))
+                input[1] = []
+                input[2] = []
+                input[3] = []
+                input[4] = []
+                input[5] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.report.collect { file(it).getName() } +
+                                process.out.data.collect { file(it).getName() } +
+                                process.out.plots.collect { file(it).getName() } +
+                                process.out.versions ).match("multiqc_stub") }
+            )
+        }
+
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/main.nf.test.snap b/modules/nf-core/multiqc/tests/main.nf.test.snap
new file mode 100644
index 0000000..7b7c132
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/main.nf.test.snap
@@ -0,0 +1,41 @@
+{
+    "multiqc_versions_single": {
+        "content": [
+            [
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-01-27T09:29:57.631982377"
+    },
+    "multiqc_stub": {
+        "content": [
+            [
+                "multiqc_report.html",
+                "multiqc_data",
+                "multiqc_plots",
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-01-27T09:30:34.743726958"
+    },
+    "multiqc_versions_config": {
+        "content": [
+            [
+                "versions.yml:md5,8f3b8c1cec5388cf2708be948c9fa42f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.2",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-01-27T09:30:21.44383553"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-core/multiqc/tests/nextflow.config b/modules/nf-core/multiqc/tests/nextflow.config
new file mode 100644
index 0000000..c537a6a
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: 'MULTIQC' {
+        ext.prefix = null
+    }
+}
diff --git a/modules/nf-core/multiqc/tests/tags.yml b/modules/nf-core/multiqc/tests/tags.yml
new file mode 100644
index 0000000..bea6c0d
--- /dev/null
+++ b/modules/nf-core/multiqc/tests/tags.yml
@@ -0,0 +1,2 @@
+multiqc:
+  - modules/nf-core/multiqc/**
diff --git a/modules/nf-neuro/betcrop/antsbet/environment.yml b/modules/nf-neuro/betcrop/antsbet/environment.yml
new file mode 100644
index 0000000..893edb3
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: betcrop_antsbet
diff --git a/modules/nf-neuro/betcrop/antsbet/main.nf b/modules/nf-neuro/betcrop/antsbet/main.nf
new file mode 100644
index 0000000..dc2867e
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/main.nf
@@ -0,0 +1,72 @@
+
+process BETCROP_ANTSBET {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(t1), path(template), path(tissues_probabilities), path(mask), path(initial_affine)
+
+    output:
+    tuple val(meta), path("*t1_bet.nii.gz")     , emit: t1
+    tuple val(meta), path("*t1_bet_mask.nii.gz"), emit: mask
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def args = []
+    if (mask) args += ["-f $mask"]
+    if (initial_affine) args += ["-r $initial_affine"]
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+    export ANTS_RANDOM_SEED=1234
+
+    antsBrainExtraction.sh -d 3 -a $t1 -o bet/ -u 0 \
+        -e $template -m $tissues_probabilities ${args.join(' ')}
+    scil_volume_math.py convert bet/BrainExtractionMask.nii.gz \
+        ${prefix}__t1_bet_mask.nii.gz --data_type uint8
+    scil_volume_math.py multiplication $t1 ${prefix}__t1_bet_mask.nii.gz \
+        ${prefix}__t1_bet.nii.gz --data_type float32
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+
+    touch ${prefix}__t1_bet.nii.gz
+    touch ${prefix}__t1_bet_mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        ants: \$(antsRegistration --version | grep "Version" | sed -E 's/.*v([0-9]+\\+\\).*/\\1/')
+    END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    antsBrainExtraction.sh
+    scil_volume_math.py -h
+
+    """
+}
diff --git a/modules/nf-neuro/betcrop/antsbet/meta.yml b/modules/nf-neuro/betcrop/antsbet/meta.yml
new file mode 100644
index 0000000..e85bfcb
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/meta.yml
@@ -0,0 +1,78 @@
+---
+name: "betcrop_antsbet"
+description: Perform Brain extraction using antsBrainExtraction.sh on T1 image.
+keywords:
+  - T1
+  - BET
+  - ants
+  - scilpy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+  - "ants":
+      description: "Advanced Normalization Tools."
+      homepage: "https://github.com/ANTsX/ANTs"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - t1:
+      type: file
+      description: Nifti t1 volume to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - template:
+      type: file
+      description: Nifti Anatomical template to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - tissues_probabilities:
+      type: file
+      description: |
+        Brain probability mask (in template space), with intensity
+        range 1 (definitely brain) to 0 (definitely background).
+      pattern: "*.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: |
+        Brain mask (in template space) used to restrict metric
+        computation when performing registration.
+      pattern: "*.{nii,nii.gz}"
+
+  - initial_affine:
+      type: file
+      description: |
+        Affine transform from T1w space to DWI space, used as
+        initialization for registration algorithms
+      pattern: "*.{mat/txt}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - t1:
+      type: file
+      description: Nifti T1 volume brain-extracted.
+      pattern: "*t1_bet.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: T1 mask brain-extracted and cropped.
+      pattern: "*t1_bet_mask.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"
diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test
new file mode 100644
index 0000000..c42aa6b
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test
@@ -0,0 +1,141 @@
+nextflow_process {
+
+    name "Test Process BETCROP_ANTSBET"
+    script "../main.nf"
+    process "BETCROP_ANTSBET"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "betcrop"
+    tag "betcrop/antsbet"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    test("betcrop - antsbet") {
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "T1w.zip", "transform.zip", "antsbet.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        t1: it.simpleName == "T1w"
+                        transform: it.simpleName == "transform"
+                        template: it.simpleName == "antsbet"
+                    }
+                ch_t1 = ch_split_test_data.t1.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_template = ch_split_test_data.template.map{
+                    test_data_directory -> [
+                        [ id: 'test' ],
+                        file("\${test_data_directory}/t1_template.nii.gz"),
+                        file("\${test_data_directory}/t1_brain_probability_map.nii.gz")
+                    ]
+                }
+                ch_mask = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template_mask.nii.gz")
+                    ]
+                }
+                ch_transform = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template.mat")
+                    ]
+                }
+                input[0] = ch_t1
+                    .join(ch_template)
+                    .join(ch_mask)
+                    .join(ch_transform)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    niftiMD5SUM(process.out.t1.get(0).get(1), 1),
+                    niftiMD5SUM(process.out.mask.get(0).get(1)),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+    test("betcrop - antsbet - stub-run") {
+        options "-stub-run"
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "T1w.zip", "transform.zip", "antsbet.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        t1: it.simpleName == "T1w"
+                        transform: it.simpleName == "transform"
+                        template: it.simpleName == "antsbet"
+                    }
+                ch_t1 = ch_split_test_data.t1.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]
+                }
+                ch_template = ch_split_test_data.template.map{
+                    test_data_directory -> [
+                        [ id: 'test' ],
+                        file("\${test_data_directory}/t1_template.nii.gz"),
+                        file("\${test_data_directory}/t1_brain_probability_map.nii.gz")
+                    ]
+                }
+                ch_mask = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template_mask.nii.gz")
+                    ]
+                }
+                ch_transform = ch_split_test_data.transform.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/t1_to_bet_template.mat")
+                    ]
+                }
+                input[0] = ch_t1
+                    .join(ch_template)
+                    .join(ch_mask)
+                    .join(ch_transform)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap
new file mode 100644
index 0000000..8777011
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/tests/main.nf.test.snap
@@ -0,0 +1,28 @@
+{
+    "betcrop - antsbet": {
+        "content": [
+            "test__t1_bet.nii.gz:md5:header,e7cfbd06624321d70cbd667a77315ba3,data,381da559c1f38a2526f58b741eb0f7fc",
+            "test__t1_bet_mask.nii.gz:md5:header,f7389fe98c9a7e3a87c90b7ca05ea14a,data,1572808125554e50ff73fbe0e28037a9",
+            [
+                "versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-15T16:55:54.33351491"
+    },
+    "betcrop - antsbet - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,bb378e913d4002d0b644d3277892ae20"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-14T20:42:47.191136661"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/betcrop/antsbet/tests/nextflow.config b/modules/nf-neuro/betcrop/antsbet/tests/nextflow.config
new file mode 100644
index 0000000..d8b1ce8
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/tests/nextflow.config
@@ -0,0 +1,6 @@
+process {
+    withName: "BETCROP_ANTSBET" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+    cpus = 1
+}
diff --git a/modules/nf-neuro/betcrop/antsbet/tests/tags.yml b/modules/nf-neuro/betcrop/antsbet/tests/tags.yml
new file mode 100644
index 0000000..e4387ae
--- /dev/null
+++ b/modules/nf-neuro/betcrop/antsbet/tests/tags.yml
@@ -0,0 +1,2 @@
+betcrop/antsbet:
+  - "modules/nf-neuro/betcrop/antsbet/**"
diff --git a/modules/nf-neuro/betcrop/synthbet/environment.yml b/modules/nf-neuro/betcrop/synthbet/environment.yml
new file mode 100644
index 0000000..4e0d7eb
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: betcrop_synthbet
diff --git a/modules/nf-neuro/betcrop/synthbet/main.nf b/modules/nf-neuro/betcrop/synthbet/main.nf
new file mode 100644
index 0000000..cbbedde
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/main.nf
@@ -0,0 +1,60 @@
+process BETCROP_SYNTHBET {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "freesurfer/freesurfer:7.4.1"
+
+    input:
+    tuple val(meta), path(image), path(weights) /* optional, input = [] */
+
+    output:
+    tuple val(meta), path("*__bet_image.nii.gz"), emit: bet_image
+    tuple val(meta), path("*__brain_mask.nii.gz"), emit: brain_mask
+    path "versions.yml"           , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def gpu = task.ext.gpu ? "--gpu" : ""
+    def border = task.ext.border ? "-b " + task.ext.border : ""
+    def nocsf = task.ext.nocsf ? "--no-csf" : ""
+    def model = "$weights" ? "--model $weights" : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=$task.cpus
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    mri_synthstrip -i $image --out ${prefix}__bet_image.nii.gz --mask ${prefix}__brain_mask.nii.gz $gpu $border $nocsf $model
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    touch ${prefix}__bet_image.nii.gz
+    touch ${prefix}__brain_mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        Freesurfer: \$(mri_convert -version | grep "freesurfer" | sed -E 's/.* ([0-9]+\\.[0-9]+\\.[0-9]+).*/\\1/')
+    END_VERSIONS
+
+    function handle_code () {
+    local code=\$?
+    ignore=( 1 )
+    exit \$([[ " \${ignore[@]} " =~ " \$code " ]] && echo 0 || echo \$code)
+    }
+    trap 'handle_code' ERR
+
+    mri_synthstrip -h
+    """
+}
diff --git a/modules/nf-neuro/betcrop/synthbet/meta.yml b/modules/nf-neuro/betcrop/synthbet/meta.yml
new file mode 100644
index 0000000..97c445d
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/meta.yml
@@ -0,0 +1,53 @@
+---
+name: "betcrop_synthbet"
+description: Perform brain extraction using synthstrip on image
+keywords:
+  - anatomical image
+  - BET
+  - freesurfer
+tools:
+  - "Freesurfer":
+      description: "Software package for the analysis and visualization of structural and functional neuroimaging data."
+      homepage: "https://surfer.nmr.mgh.harvard.edu/fswiki"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image volume to perform BET.
+      pattern: "*.{nii,nii.gz}"
+
+  - weights:
+      type: file
+      description: Alternative model weights
+      pattern: "*.pt"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - bet_image:
+      type: file
+      description: Nifti brain-extracted volume.
+      pattern: "*__bet_image.{nii,nii.gz}"
+
+  - brain_mask:
+      type: file
+      description: Brain-extracted image mask .
+      pattern: "*__brain_mask.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@anroy1"
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test
new file mode 100644
index 0000000..7e71d66
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test
@@ -0,0 +1,82 @@
+nextflow_process {
+
+    name "Test Process BETCROP_SYNTHBET"
+    script "../main.nf"
+    process "BETCROP_SYNTHBET"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "betcrop"
+    tag "betcrop/synthbet"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    test("betcrop - synthbet") {
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "freesurfer.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("betcrop - synthbet - stub-run") {
+        options "-stub-run"
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "freesurfer.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap
new file mode 100644
index 0000000..9458823
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/tests/main.nf.test.snap
@@ -0,0 +1,67 @@
+{
+    "betcrop - synthbet - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,c639461870ca534b5105f61d672f740f"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.1"
+        },
+        "timestamp": "2024-12-12T10:54:37.644838"
+    },
+    "betcrop - synthbet": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bet_image.nii.gz:md5,6f5eb365a11dfc52b8c80cd7bcee7b9d"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__brain_mask.nii.gz:md5,52871114b59d09dca864cb0ea4f12832"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,c639461870ca534b5105f61d672f740f"
+                ],
+                "bet_image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__bet_image.nii.gz:md5,6f5eb365a11dfc52b8c80cd7bcee7b9d"
+                    ]
+                ],
+                "brain_mask": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__brain_mask.nii.gz:md5,52871114b59d09dca864cb0ea4f12832"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c639461870ca534b5105f61d672f740f"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-25T18:19:01.459548926"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/nextflow.config b/modules/nf-neuro/betcrop/synthbet/tests/nextflow.config
new file mode 100644
index 0000000..a88a57d
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+    withName: "BETCROP_SYNTHBET" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        memory = 10.GB
+        ext.nocsf = true
+    }
+}
diff --git a/modules/nf-neuro/betcrop/synthbet/tests/tags.yml b/modules/nf-neuro/betcrop/synthbet/tests/tags.yml
new file mode 100644
index 0000000..34f7987
--- /dev/null
+++ b/modules/nf-neuro/betcrop/synthbet/tests/tags.yml
@@ -0,0 +1,2 @@
+betcrop/synthbet:
+  - "modules/nf-neuro/betcrop/synthbet/**"
diff --git a/modules/nf-neuro/denoising/mppca/environment.yml b/modules/nf-neuro/denoising/mppca/environment.yml
new file mode 100644
index 0000000..8d43cac
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: denoising_mppca
diff --git a/modules/nf-neuro/denoising/mppca/main.nf b/modules/nf-neuro/denoising/mppca/main.nf
new file mode 100755
index 0000000..4eb498d
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/main.nf
@@ -0,0 +1,55 @@
+
+process DENOISING_MPPCA {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "mrtrix3/mrtrix3:latest"
+
+    input:
+    tuple val(meta), path(dwi), path(mask)
+
+    output:
+    tuple val(meta), path("*_dwi_denoised.nii.gz")  , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${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=112524
+
+    dwidenoise $dwi ${prefix}_dwi_denoised.nii.gz $extent ${args.join(" ")}
+    mrcalc ${prefix}_dwi_denoised.nii.gz 0 -gt ${prefix}_dwi_denoised.nii.gz 0 \
+        -if ${prefix}_dwi_denoised.nii.gz -force
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    dwidenoise -h
+    mrcalc -h
+
+    touch ${prefix}_dwi_denoised.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        mrtrix: \$(mrcalc -version 2>&1 | sed -n 's/== mrcalc \\([0-9.]\\+\\).*/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/denoising/mppca/meta.yml b/modules/nf-neuro/denoising/mppca/meta.yml
new file mode 100755
index 0000000..5ce90fe
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/meta.yml
@@ -0,0 +1,51 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "denoising_mppca"
+description: denoise a dataset with the Marchenko-Pastur principal component analysis
+keywords:
+  - nifti
+  - denoising
+  - mppca
+  - mrtrix
+  - fsl
+tools:
+  - "MRtrix3":
+      description: "Toolbox for image processing, analysis and visualisation of dMRI."
+      homepage: "https://mrtrix.readthedocs.io/en/latest/"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - dwi:
+      type: file
+      description: Nifti dwi file to denoise
+      pattern: "*.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: Nifti mask file for the dwi, optional
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Denoised Nifti image file
+      pattern: "*_dwi_denoised.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-neuro/denoising/mppca/tests/main.nf.test b/modules/nf-neuro/denoising/mppca/tests/main.nf.test
new file mode 100644
index 0000000..42d732d
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process DENOISING_MPPCA"
+    script "../main.nf"
+    process "DENOISING_MPPCA"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "denoising"
+    tag "denoising/mppca"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    test("denoising - mppca") {
+
+        setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "raw_DWIss300-dir8.zip", "raw_segmentation.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+        when {
+            process {
+                """
+                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' ],
+                        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)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
new file mode 100644
index 0000000..21195dd
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "denoising - mppca": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dwi_denoised.nii.gz:md5,697aa941c0cb71fe1865662da5b727fa"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_dwi_denoised.nii.gz:md5,697aa941c0cb71fe1865662da5b727fa"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,adbce7b09c63d541cdc2782235363275"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.2"
+        },
+        "timestamp": "2024-12-12T18:27:14.057961679"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/denoising/mppca/tests/nextflow.config b/modules/nf-neuro/denoising/mppca/tests/nextflow.config
new file mode 100644
index 0000000..7a19d53
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/tests/nextflow.config
@@ -0,0 +1,7 @@
+process {
+    withNAME: "DENOISING_MPPCA" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.extent = 3
+    }
+    cpus = 1
+}
diff --git a/modules/nf-neuro/denoising/mppca/tests/tags.yml b/modules/nf-neuro/denoising/mppca/tests/tags.yml
new file mode 100644
index 0000000..06d15a2
--- /dev/null
+++ b/modules/nf-neuro/denoising/mppca/tests/tags.yml
@@ -0,0 +1,2 @@
+denoising/mppca:
+  - "modules/nf-neuro/denoising/mppca/**"
diff --git a/modules/nf-neuro/denoising/nlmeans/environment.yml b/modules/nf-neuro/denoising/nlmeans/environment.yml
new file mode 100644
index 0000000..7818335
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: denoising_nlmeans
diff --git a/modules/nf-neuro/denoising/nlmeans/main.nf b/modules/nf-neuro/denoising/nlmeans/main.nf
new file mode 100755
index 0000000..964b4b4
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/main.nf
@@ -0,0 +1,52 @@
+
+process DENOISING_NLMEANS {
+    tag "$meta.id"
+    label 'process_medium'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(image), path(mask)
+
+    output:
+    tuple val(meta), path("*_denoised.nii.gz")      , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def ncoils = task.ext.number_of_coils ?: 1
+    def args = ["--processes $task.cpus"]
+    if (mask) args += ["--mask $mask"]
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_denoising_nlmeans.py $image ${prefix}__denoised.nii.gz $ncoils ${args.join(" ")}
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    scil_denoising_nlmeans.py -h
+
+    touch ${prefix}_denoised.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/denoising/nlmeans/meta.yml b/modules/nf-neuro/denoising/nlmeans/meta.yml
new file mode 100755
index 0000000..23d7d1b
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/meta.yml
@@ -0,0 +1,50 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "denoising_nlmeans"
+description: denoise a dataset with the Non Local Means algorithm
+keywords:
+  - nifti
+  - denoising
+  - nlmeans
+  - scilpy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file to denoise
+      pattern: "*.{nii,nii.gz}"
+
+  - mask:
+      type: file
+      description: Nifti image file used to mask the input image
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Denoised Nifti image file
+      pattern: "*_denoised.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test b/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test
new file mode 100644
index 0000000..80baec2
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test
@@ -0,0 +1,65 @@
+nextflow_process {
+
+    name "Test Process DENOISING_NLMEANS"
+    script "../main.nf"
+    process "DENOISING_NLMEANS"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "denoising"
+    tag "denoising/nlmeans"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "raw_b0.zip", "raw_segmentation.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("denoising - nlmeans") {
+
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        b0: it.simpleName == "raw_b0"
+                        segmentation: it.simpleName == "raw_segmentation"
+                    }
+                ch_b0 = ch_split_test_data.b0.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/b0.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_b0
+                    .join(ch_mask)
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test.snap b/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test.snap
new file mode 100644
index 0000000..545bbee
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/tests/main.nf.test.snap
@@ -0,0 +1,35 @@
+{
+    "denoising - nlmeans": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__denoised.nii.gz:md5,4f679ca8c49a82ad566a814a819c6117"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,9336a0abe0f0c988b89f895943b0a153"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test__denoised.nii.gz:md5,4f679ca8c49a82ad566a814a819c6117"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,9336a0abe0f0c988b89f895943b0a153"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-05T18:28:29.498709866"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/denoising/nlmeans/tests/nextflow.config b/modules/nf-neuro/denoising/nlmeans/tests/nextflow.config
new file mode 100755
index 0000000..0293c16
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/tests/nextflow.config
@@ -0,0 +1,3 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+}
diff --git a/modules/nf-neuro/denoising/nlmeans/tests/tags.yml b/modules/nf-neuro/denoising/nlmeans/tests/tags.yml
new file mode 100644
index 0000000..7472a5b
--- /dev/null
+++ b/modules/nf-neuro/denoising/nlmeans/tests/tags.yml
@@ -0,0 +1,2 @@
+denoising/nlmeans:
+  - "modules/nf-neuro/denoising/nlmeans/**"
diff --git a/modules/nf-neuro/image/cropvolume/environment.yml b/modules/nf-neuro/image/cropvolume/environment.yml
new file mode 100644
index 0000000..670802a
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: image_cropvolume
diff --git a/modules/nf-neuro/image/cropvolume/main.nf b/modules/nf-neuro/image/cropvolume/main.nf
new file mode 100755
index 0000000..08c5d38
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/main.nf
@@ -0,0 +1,56 @@
+
+process IMAGE_CROPVOLUME {
+    tag "$meta.id"
+    label 'process_single'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(image), path(bounding_box)
+
+    output:
+    tuple val(meta), path("*_cropped.nii.gz"), emit: image
+    tuple val(meta), path("*.pkl")           , emit: bounding_box, optional: true
+    path "versions.yml"                      , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    def input_bbox = bounding_box ? "--input_bbox $bounding_box" : ""
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped"
+    def output_bbox = task.ext.output_bbox ? "--output_bbox ${prefix}_${suffix}_bbox.pkl" : ""
+
+    """
+    scil_volume_crop.py $image ${prefix}_${suffix}.nii.gz $input_bbox $output_bbox
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_cropped" : "cropped"
+
+    """
+    scil_volume_crop.py -h
+
+    touch ${prefix}_${suffix}.nii.gz
+
+    if $task.ext.output_bbox;
+    then
+        touch ${prefix}_${suffix}_bbox.pkl
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/image/cropvolume/meta.yml b/modules/nf-neuro/image/cropvolume/meta.yml
new file mode 100755
index 0000000..df13e95
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/meta.yml
@@ -0,0 +1,54 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "image_cropvolume"
+description: Crop empty planes around the data in a volume
+keywords:
+  - nifti
+  - crop
+  - scilpy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file to crop
+      pattern: "*.{nii,nii.gz}"
+
+  - bounding_box:
+      type: file
+      description: Input bounding box to use to crop the image
+      pattern: "*.{pkl}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Cropped Nifti image file
+      pattern: "*_cropped.{nii,nii.gz}"
+
+  - bounding_box:
+      type: file
+      description: Bouding box defining the limits of the crop
+      pattern: "*.pkl"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@AlexVCaron"
diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test b/modules/nf-neuro/image/cropvolume/tests/main.nf.test
new file mode 100644
index 0000000..af2c948
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test
@@ -0,0 +1,80 @@
+nextflow_process {
+
+    name "Test Process IMAGE_CROPVOLUME"
+    script "../main.nf"
+    process "IMAGE_CROPVOLUME"
+    config "./nextflow.config"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "image"
+    tag "image/cropvolume"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "heavy.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("image - cropvolume") {
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - cropvolume - outputbbox") {
+
+        config "./nextflow_bbox.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/anat/anat_image.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap
new file mode 100644
index 0000000..b7c4766
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/tests/main.nf.test.snap
@@ -0,0 +1,96 @@
+{
+    "image - cropvolume": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
+                ],
+                "bounding_box": [
+                    
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-12-12T18:59:41.317523464"
+    },
+    "image - cropvolume - outputbbox": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
+                    ]
+                ],
+                "2": [
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
+                ],
+                "bounding_box": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped_bbox.pkl:md5,d6a03b61669b07683e8c4b21a613f16c"
+                    ]
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,93cc10f69b0829409c69bf743e9c95ef"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,c9f9039fc9103e716e831016a61807f9"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-12-12T18:59:50.080977383"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow.config b/modules/nf-neuro/image/cropvolume/tests/nextflow.config
new file mode 100644
index 0000000..3a9e735
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: "IMAGE_CROPVOLUME" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}
diff --git a/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config
new file mode 100644
index 0000000..6055585
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/tests/nextflow_bbox.config
@@ -0,0 +1,6 @@
+process {
+    withName: "IMAGE_CROPVOLUME" {
+        ext.output_bbox = true
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    }
+}
diff --git a/modules/nf-neuro/image/cropvolume/tests/tags.yml b/modules/nf-neuro/image/cropvolume/tests/tags.yml
new file mode 100644
index 0000000..eeae1b2
--- /dev/null
+++ b/modules/nf-neuro/image/cropvolume/tests/tags.yml
@@ -0,0 +1,2 @@
+image/cropvolume:
+  - "modules/nf-neuro/image/cropvolume/**"
diff --git a/modules/nf-neuro/image/resample/environment.yml b/modules/nf-neuro/image/resample/environment.yml
new file mode 100644
index 0000000..5d952d2
--- /dev/null
+++ b/modules/nf-neuro/image/resample/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: image_resample
diff --git a/modules/nf-neuro/image/resample/main.nf b/modules/nf-neuro/image/resample/main.nf
new file mode 100755
index 0000000..75fb5ba
--- /dev/null
+++ b/modules/nf-neuro/image/resample/main.nf
@@ -0,0 +1,60 @@
+process IMAGE_RESAMPLE {
+    tag "$meta.id"
+    label 'process_single'
+    label 'process_high_memory'
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(image), path(ref) /* optional, input = [] */
+
+    output:
+    tuple val(meta), path("*_resampled.nii.gz") , emit: image
+    path "versions.yml"                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_resampled" : "resampled"
+    def reference = "$ref" ? "--ref $ref" : ""
+    def voxel_size = task.ext.voxel_size ? "--voxel_size " + task.ext.voxel_size : ""
+    def volume_size = task.ext.volume_size ? "--volume_size " + task.ext.volume_size : ""
+    def iso_min = task.ext.iso_min ? "--iso_min" : ""
+    def interp = task.ext.interp ? "--interp " + task.ext.interp : ""
+    def f = task.ext.f ? "-f" : ""
+    def enforce_dimensions = task.ext.enforce_dimensions ? "--enforce_dimensions" : ""
+
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+
+    scil_volume_resample.py $image ${prefix}_${suffix}.nii.gz \
+        $voxel_size $volume_size $reference $iso_min \
+        $f $enforce_dimensions $interp
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def suffix = task.ext.first_suffix ? "${task.ext.first_suffix}_resampled" : "resampled"
+    """
+    scil_volume_resample.py -h
+
+    touch ${prefix}_${suffix}.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/image/resample/meta.yml b/modules/nf-neuro/image/resample/meta.yml
new file mode 100755
index 0000000..83aabf0
--- /dev/null
+++ b/modules/nf-neuro/image/resample/meta.yml
@@ -0,0 +1,49 @@
+---
+name: "image_resample"
+description: Script to resample a dataset to match the resolution of another reference dataset or to the resolution specified in argument. Needs either one of voxel_size, volume_size, iso_min or reference as parameter/input. Interpolation defaults as linear.
+keywords:
+  - resample
+  - nifti
+  - volume
+  - scilpy
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file to resample to
+      pattern: "*.{nii,nii.gz}"
+
+  - ref:
+      type: file
+      description: Nifti reference image file
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file resampled
+      pattern: "*_resampled.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@scilus"
diff --git a/modules/nf-neuro/image/resample/tests/main.nf.test b/modules/nf-neuro/image/resample/tests/main.nf.test
new file mode 100644
index 0000000..36ba92f
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/main.nf.test
@@ -0,0 +1,191 @@
+nextflow_process {
+
+    name "Test Process IMAGE_RESAMPLE"
+    script "../main.nf"
+    process "IMAGE_RESAMPLE"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "image"
+    tag "image/resample"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "others.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("image - resample - voxsize") {
+
+        config "./nextflow_voxsize.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - resample - volsize") {
+
+        config "./nextflow_volsize.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - resample - isomin") {
+
+        config "./nextflow_isomin.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - resample - ref") {
+
+        config "./nextflow_ref.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        file("\${test_data_directory}/fa_resample.nii.gz")
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - resample - nn") {
+
+        config "./nextflow_nn.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+
+    }
+
+    test("image - resample - stub-run") {
+
+        options '-stub-run'
+
+        config "./nextflow_voxsize.config"
+
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ], // meta map
+                        file("\${test_data_directory}/fa.nii.gz"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out.versions).match() }
+            )
+        }
+
+    }
+
+}
diff --git a/modules/nf-neuro/image/resample/tests/main.nf.test.snap b/modules/nf-neuro/image/resample/tests/main.nf.test.snap
new file mode 100644
index 0000000..24e366e
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/main.nf.test.snap
@@ -0,0 +1,189 @@
+{
+    "image - resample - stub-run": {
+        "content": [
+            [
+                "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-28T18:48:51.114688771"
+    },
+    "image - resample - isomin": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,f3164907d16ceabf606a03ea0efd3a2f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T15:30:19.061192"
+    },
+    "image - resample - nn": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,8d3e1c9552673b1ce60bc4d090198564"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T15:30:42.725713"
+    },
+    "image - resample - volsize": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,7c83b666f9fb2d68643a20d1c7ac21d8"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T15:30:07.1626"
+    },
+    "image - resample - voxsize": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_voxsize_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_voxsize_resampled.nii.gz:md5,6ffdabab138186db2dab6f98ea6e9ffb"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-11-28T18:31:36.84484801"
+    },
+    "image - resample - ref": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,0a45d21ff294fda2e41c620cf83d0406"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,06181e25531a3ebdefdfd2e641a3d645"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.04.4"
+        },
+        "timestamp": "2024-10-24T15:30:31.018615"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/image/resample/tests/nextflow_isomin.config b/modules/nf-neuro/image/resample/tests/nextflow_isomin.config
new file mode 100644
index 0000000..3ffb7b6
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/nextflow_isomin.config
@@ -0,0 +1,7 @@
+process {
+    withName: "IMAGE_RESAMPLE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.iso_min = true
+        ext.interp = "lin"
+    }
+}
diff --git a/modules/nf-neuro/image/resample/tests/nextflow_nn.config b/modules/nf-neuro/image/resample/tests/nextflow_nn.config
new file mode 100644
index 0000000..1930e62
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/nextflow_nn.config
@@ -0,0 +1,7 @@
+process {
+    withName: "IMAGE_RESAMPLE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.voxel_size = 1
+        ext.interp = "nn"
+    }
+}
diff --git a/modules/nf-neuro/image/resample/tests/nextflow_ref.config b/modules/nf-neuro/image/resample/tests/nextflow_ref.config
new file mode 100644
index 0000000..f0e1beb
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/nextflow_ref.config
@@ -0,0 +1,6 @@
+process {
+    withName: "IMAGE_RESAMPLE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.interp = "lin"
+    }
+}
diff --git a/modules/nf-neuro/image/resample/tests/nextflow_volsize.config b/modules/nf-neuro/image/resample/tests/nextflow_volsize.config
new file mode 100644
index 0000000..cb892de
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/nextflow_volsize.config
@@ -0,0 +1,7 @@
+process {
+    withName: "IMAGE_RESAMPLE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.volume_size = 256
+        ext.interp = "lin"
+    }
+}
diff --git a/modules/nf-neuro/image/resample/tests/nextflow_voxsize.config b/modules/nf-neuro/image/resample/tests/nextflow_voxsize.config
new file mode 100644
index 0000000..51643e5
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/nextflow_voxsize.config
@@ -0,0 +1,7 @@
+process {
+    withName: "IMAGE_RESAMPLE" {
+        publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+        ext.voxel_size = 1
+        ext.first_suffix = "voxsize"
+    }
+}
diff --git a/modules/nf-neuro/image/resample/tests/tags.yml b/modules/nf-neuro/image/resample/tests/tags.yml
new file mode 100644
index 0000000..63487a8
--- /dev/null
+++ b/modules/nf-neuro/image/resample/tests/tags.yml
@@ -0,0 +1,2 @@
+image/resample:
+  - "modules/nf-neuro/image/resample/**"
diff --git a/modules/nf-neuro/preproc/n4/environment.yml b/modules/nf-neuro/preproc/n4/environment.yml
new file mode 100644
index 0000000..a77b1b6
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/environment.yml
@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: preproc_n4
diff --git a/modules/nf-neuro/preproc/n4/main.nf b/modules/nf-neuro/preproc/n4/main.nf
new file mode 100644
index 0000000..446ca5c
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/main.nf
@@ -0,0 +1,73 @@
+process PREPROC_N4 {
+    tag "$meta.id"
+    label 'process_medium'
+    label "process_high_memory"
+
+    container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
+        'https://scil.usherbrooke.ca/containers/scilus_2.0.2.sif':
+        'scilus/scilus:2.0.2' }"
+
+    input:
+    tuple val(meta), path(image), path(ref), path(ref_mask)
+
+    output:
+    tuple val(meta), path("*__image_n4.nii.gz")     , emit: image
+    path "versions.yml"                             , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def bspline_knot_per_voxel = task.ext.bspline_knot_per_voxel ? "$task.ext.bspline_knot_per_voxel" : "1"
+    def shrink_factor = task.ext.shrink_factor ? "$task.ext.shrink_factor" : "1"
+    """
+    export ITK_GLOBAL_DEFAULT_NUMBER_OF_THREADS=1
+    export OMP_NUM_THREADS=1
+    export OPENBLAS_NUM_THREADS=1
+    export ANTS_RANDOM_SEED=1234
+
+    if [[ -f "$ref" ]]
+    then
+        spacing=\$(mrinfo -spacing $ref | tr " " "\\n" | sort -n | tail -1)
+        knot_spacing=\$(echo "\$spacing/$bspline_knot_per_voxel" | bc -l)
+
+        N4BiasFieldCorrection -i $ref\
+            -o [${prefix}__ref_n4.nii.gz, bias_field_ref.nii.gz]\
+            -c [300x150x75x50, 1e-6] -v 1\
+            -b [\${knot_spacing}, 3] \
+            -s $shrink_factor
+
+        scil_dwi_apply_bias_field.py $image bias_field_ref.nii.gz\
+            ${prefix}__image_n4.nii.gz --mask $ref_mask -f
+
+    else
+        N4BiasFieldCorrection -i $image\
+            -o [${prefix}__image_n4.nii.gz, bias_field_t1.nii.gz]\
+            -c [300x150x75x50, 1e-6] -v 1
+    fi
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    N4BiasFieldCorrection -h
+    scil_dwi_apply_bias_field.py -h
+
+    touch ${prefix}__image_n4.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        N4BiasFieldCorrection: \$(N4BiasFieldCorrection --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}
diff --git a/modules/nf-neuro/preproc/n4/meta.yml b/modules/nf-neuro/preproc/n4/meta.yml
new file mode 100644
index 0000000..a473851
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/meta.yml
@@ -0,0 +1,54 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "preproc_n4"
+description: Bias field correction using N4
+keywords:
+  - correction
+  - N4
+  - bias field
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+
+input:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: Nifti image file to correct
+      pattern: "*.{nii,nii.gz}"
+
+  - ref:
+      type: file
+      description: Nifti image file for the reference
+      pattern: "*.{nii,nii.gz}"
+
+  - ref_mask:
+      type: file
+      description: Nifti image file mask for the reference
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - image:
+      type: file
+      description: N4 corrected image
+      pattern: "*.{nii,nii.gz}"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@arnaudbore"
diff --git a/modules/nf-neuro/preproc/n4/tests/main.nf.test b/modules/nf-neuro/preproc/n4/tests/main.nf.test
new file mode 100644
index 0000000..9cc2037
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/tests/main.nf.test
@@ -0,0 +1,69 @@
+nextflow_process {
+
+    name "Test Process PREPROC_N4"
+    script "../main.nf"
+    process "PREPROC_N4"
+
+    tag "modules"
+    tag "modules_nfcore"
+    tag "preproc"
+    tag "preproc/n4"
+
+    tag "subworkflows"
+    tag "subworkflows/load_test_data"
+
+    setup {
+            run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+                script "../../../../../subworkflows/nf-neuro/load_test_data/main.nf"
+                process {
+                    """
+                    input[0] = Channel.from( [ "heavy.zip" ] )
+                    input[1] = "test.load-test-data"
+                    """
+                }
+            }
+        }
+
+    test("preproc - n4 - dwi") {
+        config "./nextflow_dwi.config"
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ], // meta map
+                    file("\${test_data_directory}/dwi_with_b0/dwi.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/dwi_with_b0/b0.nii.gz", checkIfExists: true),
+                    file("\${test_data_directory}/dwi_with_b0/mask.nii.gz", checkIfExists: true)]}
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("preproc - n4 - anat") {
+        when {
+            process {
+                """
+                input[0] = LOAD_DATA.out.test_data_directory
+                    .map{ test_data_directory -> [
+                    [ id:'test', single_end:false ], // meta map
+                    file("\${test_data_directory}/anat/anat_image.nii.gz", checkIfExists: true),
+                    [],
+                    []]}
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+}
diff --git a/modules/nf-neuro/preproc/n4/tests/main.nf.test.snap b/modules/nf-neuro/preproc/n4/tests/main.nf.test.snap
new file mode 100644
index 0000000..9980943
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/tests/main.nf.test.snap
@@ -0,0 +1,72 @@
+{
+    "preproc - n4 - dwi": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,6383b9ffb68d04bf089ba7a040c4a77f"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,08cced153fb00b483f3a59216e05aaff"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,6383b9ffb68d04bf089ba7a040c4a77f"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,08cced153fb00b483f3a59216e05aaff"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-10T16:06:45.886061"
+    },
+    "preproc - n4 - anat": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,a0329a81f3cc26dfa04e3fb8c6e6dc66"
+                    ]
+                ],
+                "1": [
+                    "versions.yml:md5,08cced153fb00b483f3a59216e05aaff"
+                ],
+                "image": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__image_n4.nii.gz:md5,a0329a81f3cc26dfa04e3fb8c6e6dc66"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,08cced153fb00b483f3a59216e05aaff"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.8.4",
+            "nextflow": "23.10.1"
+        },
+        "timestamp": "2024-05-10T16:09:11.896134"
+    }
+}
\ No newline at end of file
diff --git a/modules/nf-neuro/preproc/n4/tests/nextflow_dwi.config b/modules/nf-neuro/preproc/n4/tests/nextflow_dwi.config
new file mode 100644
index 0000000..5c9246e
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/tests/nextflow_dwi.config
@@ -0,0 +1,6 @@
+process {
+    withName: "PREPROC_N4" {
+        ext.bspline_knot_per_voxel = 0.25
+        ext.shrink_factor = 4
+    }
+}
diff --git a/modules/nf-neuro/preproc/n4/tests/tags.yml b/modules/nf-neuro/preproc/n4/tests/tags.yml
new file mode 100644
index 0000000..c65df28
--- /dev/null
+++ b/modules/nf-neuro/preproc/n4/tests/tags.yml
@@ -0,0 +1,2 @@
+preproc/n4:
+  - "modules/nf-neuro/preproc/n4/**"
diff --git a/modules/nf-neuro/reconst/dtimetrics/main.nf b/modules/nf-neuro/reconst/dtimetrics/main.nf
index c992930..ab9609b 100644
--- a/modules/nf-neuro/reconst/dtimetrics/main.nf
+++ b/modules/nf-neuro/reconst/dtimetrics/main.nf
@@ -82,9 +82,18 @@ process RECONST_DTIMETRICS {
     scil_dti_metrics.py dwi_dti_shells.nii.gz bval_dti_shells bvec_dti_shells \
         --not_all $args $b0_threshold -f
 
+    ransac_metrics=\$(echo "$args" | awk '{for(i=1; i<NF; i++) if (\$i ~ /^--(ad|rd|md)\$/) print \$(i+1)}')
+    for metrics in \${ransac_metrics};
+    do
+        scil_volume_remove_outliers_ransac.py \${metrics} \${metrics} -f;
+    done
+
     if [ "$run_qc" = true ] && [ "$args" != '' ];
     then
-        mv ${prefix}__residual_residuals_stats.png ${prefix}__residual_residuals_stats.png_bk
+        if [ -f ${prefix}__residual_residuals_stats.png ];
+        then
+            mv ${prefix}__residual_residuals_stats.png ${prefix}__residual_residuals_stats.png_bk
+        fi
 
         nii_files=\$(echo "$args" | awk '{for(i=1; i<NF; i++) if (\$i ~ /^--(fa|ad|rd|md|rgb|residual)\$/) print \$(i+1)}')
 
@@ -127,7 +136,10 @@ process RECONST_DTIMETRICS {
 
         rm -rf *slice*
         convert -append *png ${prefix}__dti_mqc.png
-        mv ${prefix}__residual_residuals_stats.png_bk ${prefix}__residual_residuals_stats.png
+        if [ -f ${prefix}__residual_residuals_stats.png_bk ];
+        then
+            mv ${prefix}__residual_residuals_stats.png_bk ${prefix}__residual_residuals_stats.png
+        fi
     fi
 
     cat <<-END_VERSIONS > versions.yml
@@ -144,6 +156,7 @@ process RECONST_DTIMETRICS {
     """
     scil_dwi_extract_shell.py -h
     scil_dti_metrics.py -h
+    scil_volume_remove_outliers_ransac.py -h
 
     touch ${prefix}__ad.nii.gz
     touch ${prefix}__evecs.nii.gz
diff --git a/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test b/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test
index 1fa8bf8..ff88cee 100644
--- a/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test
+++ b/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test
@@ -25,6 +25,105 @@ nextflow_process {
             }
         }
 
+    test("reconst - dtimetrics") {
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        dwi: it.simpleName == "DWIss1000-dir32"
+                        segmentation: it.simpleName == "segmentation"
+                    }
+                ch_dwi = ch_split_test_data.dwi.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/dwi.nii.gz"),
+                        file("\${test_data_directory}/dwi.bval"),
+                        file("\${test_data_directory}/dwi.bvec")
+                    ]
+                }
+                ch_mask = ch_split_test_data.segmentation.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/brainmask/brainmask.nii.gz")
+                    ]
+                }
+                input[0] = ch_dwi
+                    .join(ch_mask)
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    niftiMD5SUM(process.out.ad.get(0).get(1), 6),
+                    file(process.out.mqc.get(0).get(1)).name,
+                    file(process.out.evecs.get(0).get(1)).name,
+                    file(process.out.evecs_v1.get(0).get(1)).name,
+                    file(process.out.evecs_v2.get(0).get(1)).name,
+                    file(process.out.evecs_v3.get(0).get(1)).name,
+                    niftiMD5SUM(process.out.evals.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.evals_e1.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.evals_e2.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.evals_e3.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.fa.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.ga.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.rgb.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.md.get(0).get(1), 6),
+                    file(process.out.mode.get(0).get(1)).name,
+                    niftiMD5SUM(process.out.norm.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.rd.get(0).get(1), 6),
+                    file(process.out.tensor.get(0).get(1)).name,
+                    niftiMD5SUM(process.out.nonphysical.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.pulsation_std_dwi.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.pulsation_std_b0.get(0).get(1), 6),
+                    niftiMD5SUM(process.out.residual.get(0).get(1), 2),
+                    process.out.residual_iqr_residuals,
+                    process.out.residual_mean_residuals,
+                    process.out.residual_q1_residuals,
+                    process.out.residual_q3_residuals,
+                    process.out.residual_residuals_stats,
+                    process.out.residual_std_residuals,
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
+    test("reconst - dtimetrics_with_b0mask") {
+        config "./nextflow_light.config"
+        when {
+            process {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        dwi: it.simpleName == "DWIss1000-dir32"
+                        segmentation: it.simpleName == "segmentation"
+                    }
+                input[0] = ch_split_test_data.dwi.map{
+                    test_data_directory -> [
+                        [ id:'test' ],
+                        file("\${test_data_directory}/dwi.nii.gz"),
+                        file("\${test_data_directory}/dwi.bval"),
+                        file("\${test_data_directory}/dwi.bvec"),
+                        []
+                    ]
+                }
+                """
+            }
+        }
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(
+                    niftiMD5SUM(process.out.fa.get(0).get(1), 6),
+                    process.out.versions
+                ).match() }
+            )
+        }
+    }
+
     test("reconst - stub-run dtimetrics") {
         options "-stub-run"
         when {
diff --git a/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test.snap b/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test.snap
index 02d355c..6064273 100644
--- a/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test.snap
+++ b/modules/nf-neuro/reconst/dtimetrics/tests/main.nf.test.snap
@@ -10,5 +10,100 @@
             "nextflow": "24.10.4"
         },
         "timestamp": "2025-03-06T15:57:03.763217558"
+    },
+    "reconst - dtimetrics_with_b0mask": {
+        "content": [
+            "test__fa.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,cd80bf54bc8529c97cb042d49c50d4fc",
+            [
+                "versions.yml:md5,76869f1b7075822c64ec0ff67408144a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-06T15:56:54.731216819"
+    },
+    "reconst - dtimetrics": {
+        "content": [
+            "test__ad.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,a4f053c9d65bed0062f7778818c555b4",
+            "test__dti_mqc.png",
+            "test__evecs.nii.gz",
+            "test__evecs_v1.nii.gz",
+            "test__evecs_v2.nii.gz",
+            "test__evecs_v3.nii.gz",
+            "test__evals.nii.gz:md5:header,6a667c1adb8ac1636526963bb9091ea6,data,194ed3036c73a0120615e95bc343607e",
+            "test__evals_e1.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,a4f053c9d65bed0062f7778818c555b4",
+            "test__evals_e2.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,ffa92eecb19b6ffbfb27d1696e521d44",
+            "test__evals_e3.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,7a79a34de17b0653d10242455f3b8a3a",
+            "test__fa.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,cd80bf54bc8529c97cb042d49c50d4fc",
+            "test__ga.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,a76a594121a0ef669616621eb15aec57",
+            "test__rgb.nii.gz:md5:header,952bd2b13b64d7f1b128af7d85191a18,data,a2063164b39833b2a1596683b63494bd",
+            "test__md.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,4e1b42f49af7ed531d0d85fcae5effa8",
+            "test__mode.nii.gz",
+            "test__norm.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,e4f9a5a1ea4021f01879c2ba269b33dd",
+            "test__rd.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,48d8030185bea2f3b11a0a648bbb6abd",
+            "test__tensor.nii.gz",
+            "test__nonphysical.nii.gz:md5:header,0968ff06e75bcbd0d7b2dcbcc5bf6ff7,data,4e865d417aae67c66e2a7c681aacfcae",
+            "test__pulsation_std_dwi.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,62fe8dc99a6e3733c28b2c05281b6781",
+            "test__pulsation_std_b0.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,e5bed827c14a49c4ff1aa97844ade64f",
+            "test__residual.nii.gz:md5:header,c9e720b9a8acfe45a617e6486ebb8de0,data,a01c5897af1087af9a9153e20b491e91",
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_iqr_residuals.npy:md5,58dfe3925469668723c16dc37f5c787c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_mean_residuals.npy:md5,5429f2a46c9b14efa47278c7cdb32b3c"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_q1_residuals.npy:md5,2790db91a0e7727358dd2aaccb887983"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_q3_residuals.npy:md5,15c3d97be583a3e39bad3731aaea082d"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_residuals_stats.png:md5,bb819c98e3c98a8cd74cb1e79ae044d5"
+                ]
+            ],
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test__residual_std_residuals.npy:md5,0d41ba9ad5d2ac4543f957a1d84c187f"
+                ]
+            ],
+            [
+                "versions.yml:md5,76869f1b7075822c64ec0ff67408144a"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.4"
+        },
+        "timestamp": "2025-03-06T15:56:33.450256049"
     }
-}
\ No newline at end of file
+}
diff --git a/modules/nf-neuro/reconst/dtimetrics/tests/nextflow_light.config b/modules/nf-neuro/reconst/dtimetrics/tests/nextflow_light.config
new file mode 100644
index 0000000..bd0ceaf
--- /dev/null
+++ b/modules/nf-neuro/reconst/dtimetrics/tests/nextflow_light.config
@@ -0,0 +1,22 @@
+process {
+    withName: "RECONST_DTIMETRICS" {
+        ext.ad = false
+        ext.evecs = false
+        ext.evals = false
+        ext.fa = true
+        ext.ga = false
+        ext.rgb = false
+        ext.md = false
+        ext.mode = false
+        ext.norm = false
+        ext.rd = false
+        ext.tensor = false
+        ext.nonphysical = false
+        ext.pulsation = false
+        ext.residual = false
+        ext.b0_thr_extract_b0 = 10
+        ext.dwi_shell_tolerance = 50
+        ext.max_dti_shell_value = 1200
+        ext.run_qc = true
+    }
+}
diff --git a/nextflow.config b/nextflow.config
index aa572be..30ce3f8 100644
--- a/nextflow.config
+++ b/nextflow.config
@@ -15,4 +15,62 @@ manifest {
     name            = 'scilus/nf-neuro-tutorial'
     description     = """nf-neuro-tutorial is a Nextflow pipeline for processing neuroimaging data."""
     version         = '0.1dev'
+}
+
+params.input      = false
+params.output     = 'result'
+
+// ** subworkflow PREPROC_DIFF **
+params.preproc_dwi_run_denoising = true
+
+// ** Subworkflow PREPROC T1 **
+params.preproc_t1_run_denoising = true
+params.preproc_t1_run_N4 = false
+params.preproc_t1_run_resampling = false
+params.preproc_t1_run_ants_bet = false
+params.preproc_t1_run_synthbet = true
+params.preproc_t1_run_crop = false
+
+
+process {
+
+    publishDir = [
+        path: { "${params.output}/$meta.id/${task.process.replaceAll(':', '-')}" },
+        mode: 'copy'
+    ]
+
+    withName: "DENOISING_MPPCA" {
+        ext.extent = 3
+    }
+
+    withName: "BETCROP_SYNTHBET" {
+        memory = "4G"
+        ext.nocsf = false
+    }
+
+    withName: "RECONST_DTIMETRICS" {
+        ext.ad = false
+        ext.evecs = false
+        ext.evals = false
+        ext.fa = true
+        ext.ga = false
+        ext.rgb = false
+        ext.md = false
+        ext.mode = false
+        ext.norm = false
+        ext.rd = false
+        ext.tensor = false
+        ext.nonphysical = false
+        ext.pulsation = false
+        ext.residual = false
+        ext.b0_thr_extract_b0 = 10
+        ext.dwi_shell_tolerance = 50
+        ext.max_dti_shell_value = 1200
+        ext.run_qc = true
+    }
+
+    withName: "STATS_METRICSINROI" {
+        ext.bin = true
+        ext.normalize_weights = false
+    }
 }
\ No newline at end of file
diff --git a/subworkflows/local/preproc_diff/main.nf b/subworkflows/local/preproc_diff/main.nf
new file mode 100644
index 0000000..0099ef5
--- /dev/null
+++ b/subworkflows/local/preproc_diff/main.nf
@@ -0,0 +1,45 @@
+include { RECONST_DTIMETRICS } from '../../../modules/nf-neuro/reconst/dtimetrics/main'
+include { DENOISING_MPPCA } from '../../../modules/nf-neuro/denoising/mppca/main'
+
+workflow PREPROC_DIFF {
+
+    take:
+        ch_dwi           // channel: [ val(meta), dwi, bval, bvec ]
+
+    main:
+        ch_multiqc_files = Channel.empty()
+
+        // ** Denoise DWI ** //
+        if (params.preproc_dwi_run_denoising) {
+            ch_dwi_bvalbvec = ch_dwi
+                .multiMap { meta, dwi, bval, bvec ->
+                    dwi:    [ meta, dwi ]
+                    bvs_files: [ meta, bval, bvec ]
+                }
+
+            ch_denoise_dwi = ch_dwi_bvalbvec.dwi
+                .map{ it + [[]] }
+
+            DENOISING_MPPCA ( ch_denoise_dwi )
+
+            // Fetch specific output
+            ch_dwi = DENOISING_MPPCA.out.image
+                .join(ch_dwi_bvalbvec.bvs_files)
+        }
+
+        // Input DTI update with DWI denoised output
+        input_dti = ch_dwi.map{ it + [[]] }
+
+        // DTI-derived metrics
+        RECONST_DTIMETRICS( input_dti )
+        ch_multiqc_files = ch_multiqc_files.mix(RECONST_DTIMETRICS.out.mqc)
+
+    emit:
+        dwi                 = ch_dwi_bvalbvec.dwi           // channel: [ val(meta), dwi-raw ]
+        dwi_denoised        = DENOISING_MPPCA.out.image     // channel: [ val(meta), dwi-after-mppca ]
+        bvs_files           = ch_dwi_bvalbvec.bvs_files     // channel: [ val(meta), bval, bvec ]
+        fa                  = RECONST_DTIMETRICS.out.fa     // channel: [ val(meta), fa ]
+        md                  = RECONST_DTIMETRICS.out.md     // channel: [ val(meta), md ]
+        mqc                 = ch_multiqc_files              // channel: [ val(meta), mqc ]
+
+}
\ No newline at end of file
diff --git a/subworkflows/nf-neuro/preproc_t1/main.nf b/subworkflows/nf-neuro/preproc_t1/main.nf
new file mode 100644
index 0000000..cc87f85
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/main.nf
@@ -0,0 +1,159 @@
+// ** Importing modules from nf-neuro ** //
+include { DENOISING_NLMEANS } from '../../../modules/nf-neuro/denoising/nlmeans/main'
+include { PREPROC_N4 } from '../../../modules/nf-neuro/preproc/n4/main'
+include { IMAGE_RESAMPLE } from '../../../modules/nf-neuro/image/resample/main'
+include { BETCROP_ANTSBET } from '../../../modules/nf-neuro/betcrop/antsbet/main'
+include { BETCROP_SYNTHBET} from '../../../modules/nf-neuro/betcrop/synthbet/main'
+include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_T1 } from '../../../modules/nf-neuro/image/cropvolume/main'
+include { IMAGE_CROPVOLUME as IMAGE_CROPVOLUME_MASK } from '../../../modules/nf-neuro/image/cropvolume/main'
+
+params.preproc_t1_run_synthbet = false
+
+workflow PREPROC_T1 {
+
+    take:
+        ch_image            // channel: [ val(meta), image ]
+        ch_template         // channel: [ val(meta), template ]                              , optional
+        ch_probability_map  // channel: [ val(meta), probability-map, mask, initial-affine ] , optional
+        ch_mask_nlmeans     // channel: [ val(meta), mask ]                                  , optional
+        ch_ref_n4           // channel: [ val(meta), ref, ref-mask ]                         , optional
+        ch_ref_resample     // channel: [ val(meta), ref ]                                   , optional
+        ch_weights          // channel: [ val(meta), weights ]                               , optional
+
+    main:
+
+        ch_versions = Channel.empty()
+
+        if ( params.preproc_t1_run_denoising ) {
+
+            // ** Denoising ** //
+            // Result : [ meta, image, mask | [] ]
+            //  Steps :
+            //   - join [ meta, image, mask | null ]
+            //   - map  [ meta, image, mask | [] ]
+            ch_nlmeans = ch_image
+                .join(ch_mask_nlmeans, remainder: true)
+                .map{ it[0..1] + [it[2] ?: []] }
+
+            DENOISING_NLMEANS ( ch_nlmeans )
+            ch_versions = ch_versions.mix(DENOISING_NLMEANS.out.versions.first())
+            image_nlmeans = DENOISING_NLMEANS.out.image
+        }
+        else {
+            image_nlmeans = ch_image
+        }
+
+        if ( params.preproc_t1_run_N4 ) {
+            // ** N4 correction ** //
+            // Result : [ meta, image, reference | [], mask | [] ]
+            //  Steps :
+            //   - join [ meta, image ] + [ reference, mask ] | [ reference, null ] | [ null ]
+            //   - map  [ meta, image, reference | [], mask | [] ]
+            //   - join [ meta, image, reference | [], mask | [], nlmeans-mask | null ]
+            //   - map  [ meta, image, reference | [], mask | [] ]
+            ch_N4 = image_nlmeans
+                .join(ch_ref_n4, remainder: true)
+                .map{ it[0..1] + [it[2] ?: [], it[3] ?: []] }
+                .join(ch_mask_nlmeans, remainder: true)
+                .map{ it[0..2] + [it[3] ?: it[4] ?: []] }
+
+            PREPROC_N4 ( ch_N4 )
+            ch_versions = ch_versions.mix(PREPROC_N4.out.versions.first())
+            image_N4 = PREPROC_N4.out.image
+        }
+        else {
+            image_N4 = image_nlmeans
+        }
+
+        if ( params.preproc_t1_run_resampling ) {
+            // ** Resampling ** //
+            // Result : [ meta, image, reference | [] ]
+            //  Steps :
+            //   - join [ meta, image, reference | null ]
+            //   - map  [ meta, image, reference | [] ]
+            ch_resampling = image_N4
+                .join(ch_ref_resample, remainder: true)
+                .map{ it[0..1] + [it[2] ?: []] }
+
+            IMAGE_RESAMPLE ( ch_resampling )
+            ch_versions = ch_versions.mix(IMAGE_RESAMPLE.out.versions.first())
+            image_resample = IMAGE_RESAMPLE.out.image
+        }
+        else {
+            image_resample = image_N4
+        }
+
+        if ( params.preproc_t1_run_synthbet ) {
+            // ** SYNTHBET ** //
+            // Result : [ meta, image, weights | [] ]
+            //  Steps :
+            //   - join [ meta, image, weights | null ]
+            //   - map  [ meta, image, weights | [] ]
+            ch_bet = image_resample
+                .join(ch_weights, remainder: true)
+                .map{ it[0..1] + [it[2] ?: []] }
+
+            BETCROP_SYNTHBET ( ch_bet )
+            ch_versions = ch_versions.mix(BETCROP_SYNTHBET.out.versions.first())
+
+            // ** Setting BET output ** //
+            image_bet = BETCROP_SYNTHBET.out.bet_image
+            mask_bet = BETCROP_SYNTHBET.out.brain_mask
+        }
+        else if ( params.preproc_t1_run_ants_bet ) {
+            // ** ANTSBET ** //
+            // The template and probability maps are mandatory if running antsBET. Since the
+            // error message from nextflow when they are absent is either non-informative or
+            // missing, we use ifEmpty to provide a more informative one.
+            ch_bet = image_resample
+                .join(ch_template.ifEmpty{ error("ANTS BET needs a template") })
+                .join(ch_probability_map.ifEmpty{ error("ANTS BET needs a tissue probability map") })
+                .map{ it + [[], []] }
+
+            BETCROP_ANTSBET ( ch_bet )
+            ch_versions = ch_versions.mix(BETCROP_ANTSBET.out.versions.first())
+
+            // ** Setting BET output ** //
+            image_bet = BETCROP_ANTSBET.out.t1
+            mask_bet = BETCROP_ANTSBET.out.mask
+        }
+        else {
+            image_bet = image_resample
+            mask_bet = Channel.empty()
+        }
+
+        if ( params.preproc_t1_run_crop ) {
+            // ** Crop image ** //
+            ch_crop = image_bet
+                .map{ it + [[]] }
+
+            IMAGE_CROPVOLUME_T1 ( ch_crop )
+            ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_T1.out.versions.first())
+            image_crop = IMAGE_CROPVOLUME_T1.out.image
+            bbox = IMAGE_CROPVOLUME_T1.out.bounding_box
+
+            // ** Crop mask ** //
+            ch_crop_mask = mask_bet
+                .join(IMAGE_CROPVOLUME_T1.out.bounding_box)
+
+            IMAGE_CROPVOLUME_MASK ( ch_crop_mask )
+            ch_versions = ch_versions.mix(IMAGE_CROPVOLUME_MASK.out.versions.first())
+            mask_crop = IMAGE_CROPVOLUME_MASK.out.image
+        }
+        else {
+            image_crop = image_bet
+            mask_crop = Channel.empty()
+            bbox = Channel.empty()
+        }
+
+    emit:
+        t1_final        = image_crop                    // channel: [ val(meta), t1-preprocessed ]
+        mask_final      = mask_crop                     // channel: [ val(meta), t1-mask ]
+        image_nlmeans   = image_nlmeans                 // channel: [ val(meta), t1-after-denoise ]
+        image_N4        = image_N4                      // channel: [ val(meta), t1-after-unbias ]
+        image_resample  = image_resample                // channel: [ val(meta), t1-after-resample ]
+        image_bet       = image_bet                     // channel: [ val(meta), t1-after-bet ]
+        mask_bet        = mask_bet                      // channel: [ val(meta), intermediary-mask ]
+        crop_box        = bbox                          // channel: [ val(meta), bounding-box ]
+        versions        = ch_versions                   // channel: [ versions.yml ]
+}
diff --git a/subworkflows/nf-neuro/preproc_t1/meta.yml b/subworkflows/nf-neuro/preproc_t1/meta.yml
new file mode 100644
index 0000000..e736187
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/meta.yml
@@ -0,0 +1,151 @@
+name: "preproc_t1"
+description: |
+  Subworkflow for T1 image pre-processing, from denoising to brain extraction and cropping.
+  It requires three input channels, one with a raw T1 image you want to process (ch_image),
+  one with a T1 template (ch_template) and one with a brain probability mask (ch_probability_map).
+  The aim of the workflow is to carry out the first stages of pre-processing, through denoising,
+  N4 correction, resampling and brain extraction, right up to the cropping stage.
+  The resulting T1 is corrected, resampled, brain extracted and cropped.
+  You can retrieve the file after each step if you don't want to run the entire subworkflow.
+  The next steps would be to register the resulting T1-corrected image with the DWI-corrected image
+  with, for example, the REGISTRATION subworkflow. IMPORTANT : the subworkflow is only reproducible
+  with when running ANTs BET using a single thread.
+  -----------  Steps  -----------
+  Denoising (nlmeans, scil).
+    Used to remove the noise induced by the MRI acquisition,
+    enhance the signal to noise ratio and improve the image quality and following metrics.
+    The denoising is performed in the original spatial resolution and uses the nlmeans method.
+  N4 Image Intensities Bias Correction (N4BiasFieldCorrection, ANTs).
+    Used to normalize the image intensities and reduce biases (e.g. signal loss with distance in
+    multi-channel head coils), while preserving contrasts between tissues.
+  Resample (DIPY).
+    Resamples the T1 to an isotropic spatial resolution. The default is 1mm, a standard in humans which
+    usually facilitate registration with corrected DWI images.
+    This spatial resolution is modifiable in the configuration file.
+  Brain Extraction (ANTs - default, freesurfer).
+    Isolates the brain tissue voxels from the remaining image. Also creates a binary brain mask.
+    This brain extraction is required for the T1 to DWI Registration. IMPORTANT : when using ANTs,
+    brain extraction is reproducible only when run using a single thread.
+  Cropping (scil).
+    Crops the empty planes around the brain to optimize the next processing steps.
+  Subworkflow based on Tractoflow : https://www.sciencedirect.com/science/article/pii/S105381192030375X?via%3Dihub
+
+keywords:
+  - T1
+  - preprocessing
+  - nlmeans
+  - n4
+  - resample
+  - bet
+  - crop
+
+components:
+  - denoising/nlmeans
+  - preproc/n4
+  - image/resample
+  - betcrop/antsbet
+  - betcrop/synthbet
+  - image/cropvolume
+
+input:
+  - ch_image:
+      type: file
+      description: |
+        The input channel containing the anatomical image.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_template:
+      type: file
+      description: |
+        The input channel containing the anatomical template for antsBET.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_probability_map:
+      type: file
+      description: |
+        The input channel containing the brain probability mask for antsBET,
+        with intensity range 1 (definitely brain) to 0 (definitely background).
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_mask_nlmeans:
+      type: file
+      description: |
+        The input channel containing the brain mask for the nlmeans denoising. Optional
+        Structure: [ val(meta), path(mask) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_ref_n4:
+      type: file
+      description: |
+        The input channel containing the reference and the reference mask for the n4 correction. Optional
+        Structure: [ val(meta), path(ref), path(mask_ref) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_ref_resample:
+      type: file
+      description: |
+        The input channel containing the reference for the resampling. Optional
+        Structure: [ val(meta), path(ref) ]
+      pattern: "*.{nii,nii.gz}"
+  - ch_weights:
+      type: file
+      description: |
+        The input channel containing an alternative model weights for synthbet. Optional
+        Structure: [ val(meta), path (weights)]
+      pattern: "*.pt"
+output:
+  - image_nlmeans:
+      type: file
+      description: |
+        Channel containing the anatomical image after the nlmeans denoising.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - image_N4:
+      type: file
+      description: |
+        Channel containing the anatomical image after the N4 correction.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - image_resample:
+      type: file
+      description: |
+        Channel containing the anatomical image after the resampling.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - image_bet:
+      type: file
+      description: |
+        Channel containing the anatomical image after the brain-extraction.
+        Structure: [ val(meta), path(t1) ]
+      pattern: "*.{nii,nii.gz}"
+  - mask_bet:
+      type: file
+      description: |
+        Channel containing the binary mask after the brain-extraction.
+        Structure: [ val(meta), path(mask) ]
+      pattern: "*.{nii,nii.gz}"
+  - crop_box:
+      type: file
+      description: |
+        Channel containing the bouding box defining the limits of the crop.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{pkl}"
+  - mask_final:
+      type: file
+      description: |
+        Channel containing the binary mask after the all preprocessing.
+        Structure: [ val(meta), path(mask) ]
+      pattern: "*.{nii,nii.gz}"
+  - t1_final:
+      type: file
+      description: |
+        Channel containing the anatomical image after the all preprocessing.
+        Structure: [ val(meta), path(image) ]
+      pattern: "*.{nii,nii.gz}"
+  - versions:
+      type: file
+      description: |
+        File containing software versions
+        Structure: [ path(versions.yml) ]
+      pattern: "versions.yml"
+
+authors:
+  - "@ThoumyreStanislas"
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test
new file mode 100644
index 0000000..ec2d95b
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test
@@ -0,0 +1,341 @@
+nextflow_workflow {
+
+    name "Test Subworkflow PREPROC_T1"
+    script "../main.nf"
+    workflow "PREPROC_T1"
+
+    tag "subworkflows"
+    tag "subworkflows_nfcore"
+    tag "subworkflows/preproc_t1"
+
+    tag "denoising/nlmeans"
+    tag "preproc/n4"
+    tag "image/resample"
+    tag "betcrop/antsbet"
+    tag "betcrop/synthbet"
+    tag "image/cropvolume"
+
+    tag "load_test_data"
+
+    setup {
+        run("LOAD_TEST_DATA", alias: "LOAD_DATA") {
+            script "../../load_test_data/main.nf"
+            process {
+                """
+                input[0] = Channel.from( [ "antsbet.zip" , "T1w.zip" ] )
+                input[1] = "test.load-test-data"
+                """
+            }
+        }
+    }
+
+    test("preproc_t1_antsbet_error") {
+        config "./nextflow.config"
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        t1w: it.simpleName == "T1w"
+                    }
+                input[0] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]}
+                input[1] = Channel.empty()
+                input[2] = Channel.empty()
+                input[3] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assert workflow.failed
+        }
+    }
+
+    test("preproc_t1_antsbet") {
+        config "./nextflow.config"
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        t1w: it.simpleName == "T1w"
+                    }
+                input[0] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]}
+                input[1] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/t1_template.nii.gz")
+                    ]}
+                input[2] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/t1_brain_probability_map.nii.gz"),
+                        [],
+                        []
+                    ]}
+                input[3] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.image_nlmeans.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.image_N4.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.image_resample.get(0).get(1)),
+                    file(workflow.out.image_bet.get(0).get(1)).name,
+                    file(workflow.out.mask_bet.get(0).get(1)).name,
+                    file(workflow.out.crop_box.get(0).get(1)).name,
+                    file(workflow.out.mask_final.get(0).get(1)).name,
+                    file(workflow.out.t1_final.get(0).get(1)).name,
+                    workflow.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("preproc_t1_synthbet") {
+        config "./nextflow_synthbet.config"
+
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        t1w: it.simpleName == "T1w"
+                    }
+                input[0] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]}
+                input[1] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[2] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[3] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        [],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success},
+                { assert snapshot(
+                    niftiMD5SUM(workflow.out.image_nlmeans.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.image_N4.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.image_resample.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.image_bet.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.mask_bet.get(0).get(1)),
+                    workflow.out.crop_box,
+                    niftiMD5SUM(workflow.out.mask_final.get(0).get(1)),
+                    niftiMD5SUM(workflow.out.t1_final.get(0).get(1)),
+                    workflow.out.versions
+                ).match()}
+            )
+        }
+    }
+
+    test("preproc_t1_quick") {
+        config "./nextflow_quick.config"
+
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        t1w: it.simpleName == "T1w"
+                    }
+                input[0] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]}
+                input[1] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[2] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[3] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        [],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+
+    test("preproc_t1_skip_all") {
+        config "./nextflow_skip_all.config"
+
+        when {
+            workflow {
+                """
+                ch_split_test_data = LOAD_DATA.out.test_data_directory
+                    .branch{
+                        antsbet: it.simpleName == "antsbet"
+                        t1w: it.simpleName == "T1w"
+                    }
+                input[0] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        file("\${test_data_directory}/T1w.nii.gz")
+                    ]}
+                input[1] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[2] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[3] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        [],
+                        []
+                    ]}
+                input[4] = ch_split_test_data.t1w.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        [],
+                        []
+                    ]}
+                input[5] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                input[6] = ch_split_test_data.antsbet.map{
+                    test_data_directory -> [
+                        [ id:'test', single_end:false ],
+                        []
+                    ]}
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert workflow.success },
+                { assert snapshot(workflow.out).match() }
+            )
+        }
+    }
+}
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
new file mode 100644
index 0000000..da31b7d
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/main.nf.test.snap
@@ -0,0 +1,314 @@
+{
+    "preproc_t1_quick": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__denoised.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__denoised.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "6": [
+
+                ],
+                "7": [
+
+                ],
+                "8": [
+                    "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
+                    "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20",
+                    "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
+                ],
+                "crop_box": [
+
+                ],
+                "image_N4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__denoised.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "image_bet": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "image_nlmeans": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test__denoised.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "image_resample": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_resampled.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "mask_bet": [
+
+                ],
+                "mask_final": [
+
+                ],
+                "t1_final": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "test_cropped.nii.gz:md5,c507c9182cc410c298fad4a03540c0c9"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
+                    "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20",
+                    "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-14T10:02:29.972139887"
+    },
+    "preproc_t1_synthbet": {
+        "content": [
+            "test__denoised.nii.gz:md5:header,a7ee0e819007aba98d14f7a145b550e6,data,2e21433e2bcd4de2a6b6167c6233cd40",
+            "test__image_n4.nii.gz:md5:header,e7cfbd06624321d70cbd667a77315ba3,data,a81e98f32ed963c098ccb07486101898",
+            "test_resampled.nii.gz:md5:header,7628a07204938d640c3530fa3d76d2b7,data,a81e98f32ed963c098ccb07486101898",
+            "test__bet_image.nii.gz:md5:header,38a09a5addf7c1f13dae1121c562f3b5,data,74f76699e09839809038875af1d9ae6c",
+            "test__brain_mask.nii.gz:md5:header,8fc2b4ae979d881623dfd34d377d437d,data,2d61506dc4ab2f8093b731474ae7e45c",
+            [
+                [
+                    {
+                        "id": "test",
+                        "single_end": false
+                    },
+                    "test_t1_cropped_bbox.pkl:md5,522d2c44d3ad1058ea77457a263e39c8"
+                ]
+            ],
+            "test_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,e551be653d402018fd73a4f708b1641e",
+            "test_t1_cropped.nii.gz:md5:header,efab188f3700b5b29d4b4ef99cec1295,data,8a93b9d76ead7dae4af4792b9cf70479",
+            [
+                "versions.yml:md5,318cabe934be45528a25f52083d9c90d",
+                "versions.yml:md5,b979132991d8f72a3585465533bd5730",
+                "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
+                "versions.yml:md5,be3dbb0ac2589ad263d583018f339102",
+                "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20",
+                "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-11-25T18:23:03.990173398"
+    },
+    "preproc_t1_skip_all": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "1": [
+
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "3": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "5": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "6": [
+
+                ],
+                "7": [
+
+                ],
+                "8": [
+
+                ],
+                "crop_box": [
+
+                ],
+                "image_N4": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "image_bet": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "image_nlmeans": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "image_resample": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "mask_bet": [
+
+                ],
+                "mask_final": [
+
+                ],
+                "t1_final": [
+                    [
+                        {
+                            "id": "test",
+                            "single_end": false
+                        },
+                        "T1w.nii.gz:md5,ce10054d30c0a0753c619d67d811fe32"
+                    ]
+                ],
+                "versions": [
+
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.3"
+        },
+        "timestamp": "2025-01-14T21:44:26.607236449"
+    },
+    "preproc_t1_antsbet": {
+        "content": [
+            "test__denoised.nii.gz:md5:header,a7ee0e819007aba98d14f7a145b550e6,data,2e21433e2bcd4de2a6b6167c6233cd40",
+            "test__image_n4.nii.gz:md5:header,e7cfbd06624321d70cbd667a77315ba3,data,a81e98f32ed963c098ccb07486101898",
+            "test_resampled.nii.gz:md5:header,7628a07204938d640c3530fa3d76d2b7,data,a81e98f32ed963c098ccb07486101898",
+            "test__t1_bet.nii.gz",
+            "test__t1_bet_mask.nii.gz",
+            "test_t1_cropped_bbox.pkl",
+            "test_cropped.nii.gz",
+            "test_t1_cropped.nii.gz",
+            [
+                "versions.yml:md5,b979132991d8f72a3585465533bd5730",
+                "versions.yml:md5,bdd934b4b8456060c36d6d97e4f30740",
+                "versions.yml:md5,be3dbb0ac2589ad263d583018f339102",
+                "versions.yml:md5,bf4dd58c38dd4863ebfb9e78a94c3a20",
+                "versions.yml:md5,da278daafbe3afa8454021e2716dd205",
+                "versions.yml:md5,ea32c30f5320f720b2f5dc32ac2535ea"
+            ]
+        ],
+        "meta": {
+            "nf-test": "0.9.0",
+            "nextflow": "24.10.0"
+        },
+        "timestamp": "2024-12-12T15:50:29.838128539"
+    }
+}
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config
new file mode 100644
index 0000000..3a82000
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow.config
@@ -0,0 +1,18 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "IMAGE_RESAMPLE" {
+        ext.voxel_size = 1
+        ext.interp = "lin"
+    }
+    withName: "IMAGE_CROPVOLUME_T1" {
+        ext.output_bbox = true
+        ext.first_suffix = "t1"
+    }
+}
+
+params.preproc_t1_run_denoising = true
+params.preproc_t1_run_N4 = true
+params.preproc_t1_run_resampling = true
+params.preproc_t1_run_ants_bet = true
+params.preproc_t1_run_synthbet = false
+params.preproc_t1_run_crop = true
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_quick.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_quick.config
new file mode 100644
index 0000000..04551ce
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_quick.config
@@ -0,0 +1,14 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "IMAGE_RESAMPLE" {
+        ext.voxel_size = 1
+        ext.interp = "lin"
+    }
+}
+
+params.preproc_t1_run_denoising = true
+params.preproc_t1_run_N4 = false
+params.preproc_t1_run_resampling = true
+params.preproc_t1_run_ants_bet = false
+params.preproc_t1_run_synthbet = false
+params.preproc_t1_run_crop = true
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_skip_all.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_skip_all.config
new file mode 100644
index 0000000..4e87743
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_skip_all.config
@@ -0,0 +1,14 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "BETCROP_SYNTHBET" {
+        memory = "8G"
+        ext.nocsf = true
+    }
+}
+
+params.preproc_t1_run_denoising = false
+params.preproc_t1_run_N4 = false
+params.preproc_t1_run_resampling = false
+params.preproc_t1_run_ants_bet = false
+params.preproc_t1_run_synthbet = false
+params.preproc_t1_run_crop = false
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config
new file mode 100644
index 0000000..a514910
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/nextflow_synthbet.config
@@ -0,0 +1,22 @@
+process {
+    publishDir = { "${params.outdir}/${task.process.tokenize(':')[-1].tokenize('_')[0].toLowerCase()}" }
+    withName: "IMAGE_RESAMPLE" {
+        ext.voxel_size = 1
+        ext.interp = "lin"
+    }
+    withName: "IMAGE_CROPVOLUME_T1" {
+        ext.output_bbox = true
+        ext.first_suffix = "t1"
+    }
+    withName: "BETCROP_SYNTHBET" {
+        memory = "8G"
+        ext.nocsf = true
+    }
+}
+
+params.preproc_t1_run_denoising = true
+params.preproc_t1_run_N4 = true
+params.preproc_t1_run_resampling = true
+params.preproc_t1_run_ants_bet = false
+params.preproc_t1_run_synthbet = true
+params.preproc_t1_run_crop = true
diff --git a/subworkflows/nf-neuro/preproc_t1/tests/tags.yml b/subworkflows/nf-neuro/preproc_t1/tests/tags.yml
new file mode 100644
index 0000000..033e4cd
--- /dev/null
+++ b/subworkflows/nf-neuro/preproc_t1/tests/tags.yml
@@ -0,0 +1,2 @@
+subworkflows/preproc_t1:
+  - subworkflows/nf-neuro/preproc_t1/**