Invivo

.gitignore

@@ -0,0 +1 @@
+.DS_Store

main.nf

@@ -3,6 +3,7 @@ include { DENOISING_MPPCA } from './modules/nf-neuro/denoising/mppca/main.nf'
 include { PREPROC_SINGLEEDDY } from './modules/local/preproc/singleeddy/main.nf'
 include { UTILS_EXTRACTB0 } from './modules/nf-neuro/utils/extractb0/main.nf'
 include { NNUNET } from './subworkflows/local/nnunet/'
+include { BET } from './subworkflows/local/bet/main.nf'
 include { MOUSE_N4 } from './modules/local/mouse/n4/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_DWI} from './modules/nf-neuro/image/resample/main.nf'
 include { IMAGE_RESAMPLE as RESAMPLE_MASK} from './modules/nf-neuro/image/resample/main.nf'
@@ -36,13 +37,17 @@ workflow get_data {
             log.info ""
             log.info "                         [input]"
             log.info "                           ├-- S1"
-            log.info "                           |   ├-- *dwi.nii.gz"
             log.info "                           |   ├-- *dwi.bval"
-            log.info "                           |   └-- *dwi.bvec"
+            log.info "                           |   ├-- *dwi.bvec"
+            log.info "                           |   ├-- *dwi.nii.gz"
+            log.info "                           |   ├-- *anat.nii.gz (optional)"
+            log.info "                           |   └-- *mask.nii.gz (optional)"
             log.info "                           └-- S2"
-            log.info "                                ├-- *dwi.nii.gz"
-            log.info "                                ├-- *dwi.bval"
-            log.info "                                └-- *dwi.bvec"
+            log.info "                               ├-- *dwi.bval"
+            log.info "                               ├-- *dwi.bvec"
+            log.info "                               ├-- *dwi.nii.gz"
+            log.info "                               ├-- *anat.nii.gz (optional)"
+            log.info "                               └-- *mask.nii.gz (optional)"
             log.info ""
             log.info ""
             error "Please resubmit your command with the previous file structure."
@@ -57,6 +62,10 @@ workflow get_data {
                         .map { mask_file -> def sid = mask_file.parent.name
                         [[id: sid], mask_file] }
 
+        anat_channel = Channel.fromPath("$input/**/*anat.nii.gz")
+                        .map { anat_file -> def sid = anat_file.parent.name
+                        [[id: sid], anat_file] }
+
         template_channel = Channel.fromPath("$projectDir/assets/reference_rgb_mqc.png")
 
         lut_channel = Channel.of([
@@ -68,6 +77,7 @@ workflow get_data {
     emit:
         dwi   = dwi_channel
         mask  = mask_channel
+        anat = anat_channel
         template_rgb = template_channel
         lut = lut_channel
 }
@@ -96,6 +106,8 @@ workflow {
         }
     ch_ref_rgb = data.template_rgb
     ch_lut = data.lut
+    ch_bet = data.anat
+    ch_mask = Channel.empty()
 
     if ( params.run_preqc ) {
         PRE_QC(ch_dwi_bvalbvec.dwi.join(ch_dwi_bvalbvec.bvs_files).combine(ch_ref_rgb))
@@ -105,6 +117,7 @@ workflow {
             log.warn('Using the output from the preqc module is highly experimental. Please be careful.')
             ch_after_preqc = PRE_QC.out.dwi
             bvs_after_preqc = PRE_QC.out.bvs
+
         }
         else {
             ch_after_preqc = Channel.empty()
@@ -136,21 +149,31 @@ workflow {
     else {
         ch_after_eddy = ch_eddy
     }
-
     UTILS_EXTRACTB0(ch_after_eddy)
-    ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
-    .join(data.mask, by: 0, remainder: true)
-            .map { meta, dwi, bval, bvec, b0, mask ->   
-                [meta, dwi, bval, b0, mask ?: [   ]]}  // Use empty list if mask is null
-
-    NNUNET(ch_nnunet)
+
+    if (params.invivo) {
+        BET(ch_bet)
+        ch_mask = BET.out.mask
+    }
+    else if ( params.data_masked ) {
+        ch_mask = data.mask
+    }
+    else {
+        ch_nnunet = ch_after_eddy.join(UTILS_EXTRACTB0.out.b0)
+                .map { meta, dwi, bval, bvec, b0 ->   
+                    [meta, dwi, bval, b0 ?: [   ]]}
+
+        NNUNET(ch_nnunet)
+
+        ch_mask = NNUNET.out.mask
+    }
 
     if ( params.run_n4 ) {
         ch_N4 = ch_after_eddy
             .map{ meta, dwi, _bval, _bvec ->
                     tuple(meta, dwi)}
             .join(UTILS_EXTRACTB0.out.b0)
-            .join(NNUNET.out.mask)
+            .join(ch_mask)
         MOUSE_N4(ch_N4)
         ch_after_n4 = MOUSE_N4.out.dwi_n4
     }
@@ -161,15 +184,15 @@ workflow {
 
     if ( params.run_resampling ) {
         RESAMPLE_DWI(ch_after_n4.map{ meta, dwi -> [meta, dwi, []] }) // Add an empty list for the optional reference image
-        RESAMPLE_MASK(NNUNET.out.mask.map{ meta, mask -> [meta, mask, []] })
+        RESAMPLE_MASK(ch_mask.map{ meta, mask -> [meta, mask, []] })
         IMAGE_CONVERT(RESAMPLE_MASK.out.image)
 
         dwi_after_resample = RESAMPLE_DWI.out.image
         mask_after_resample = IMAGE_CONVERT.out.image
     }
     else {
         dwi_after_resample = ch_after_n4
-        IMAGE_CONVERT(NNUNET.out.mask)
+        IMAGE_CONVERT(ch_mask)
         mask_after_resample = IMAGE_CONVERT.out.image
     }
 
@@ -187,13 +210,15 @@ workflow {
     ch_multiqc_files = ch_multiqc_files.mix(RECONST_DTIMETRICS.out.mqc)
 
     /* FODF */ 
-    RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
-    ch_for_reconst_fodf = ch_for_reconst
-                            .join(RECONST_DTIMETRICS.out.fa)
-                            .join(RECONST_DTIMETRICS.out.md)
-                            .join(RECONST_FRF.out.frf)
-                            .map{ it + [[], []]}
-    RECONST_FODF(ch_for_reconst_fodf)
+    if ( params.run_fodf_metrics ) {
+        RECONST_FRF(ch_for_reconst.map{ it + [[], [], []]})
+        ch_for_reconst_fodf = ch_for_reconst
+                                .join(RECONST_DTIMETRICS.out.fa)
+                                .join(RECONST_DTIMETRICS.out.md)
+                                .join(RECONST_FRF.out.frf)
+                                .map{ it + [[], []]}
+        RECONST_FODF(ch_for_reconst_fodf)
+    }
 
     /* QBALL */
     RECONST_QBALL(ch_for_reconst)

modules/local/mouse/betnnunet/main.nf

@@ -5,7 +5,7 @@ process MOUSE_BETNNUNET {
     container "scilus/nnunet_bet_mouse:0.1.0_cpu"
 
     input:
-        tuple val(meta), path(dwi), path(b0), path(mask)
+        tuple val(meta), path(dwi), path(b0)
     output:
         tuple val(meta), path("*__mask.nii.gz")      , emit: mask
         path "versions.yml"                          , emit: versions
@@ -17,21 +17,16 @@ process MOUSE_BETNNUNET {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    if [[ -f "$mask" ]]
-    then
-        mv $mask ${prefix}__mask.nii.gz
-    else
 	export nnUNet_raw="Database/RAW/"
 	export nnUNet_preprocessed="Database/PRE/"
 	export nnUNet_results="Database/RESULTS/"
-        mkdir -p Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs
-        ln -s /Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json
-        ln -s /Database/RESULTS Database/RESULTS
-        mv $b0 Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0000.nii.gz
-        mv $dwi Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0001.nii.gz
-        nnUNetv2_predict -i Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs -o ./ -d 012 -c 3d_fullres -f all -npp 1 -nps 1 -device 'cpu' -tr nnUNetTrainer -chk checkpoint_best.pth
-        mv exvivobrain_000.nii.gz ${prefix}__mask.nii.gz
-    fi  
+    mkdir -p Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs
+    ln -s /Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json Database/RAW/Dataset012_ExVivoBrainFSboth/dataset.json
+    ln -s /Database/RESULTS Database/RESULTS
+    mv $b0 Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0000.nii.gz
+    mv $dwi Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs/exvivobrain_000_0001.nii.gz
+    nnUNetv2_predict -i Database/RAW/Dataset012_ExVivoBrainFSboth/imagesTs -o ./ -d 012 -c 3d_fullres -f all -npp 1 -nps 1 -device 'cpu' -tr nnUNetTrainer -chk checkpoint_best.pth
+    mv exvivobrain_000.nii.gz ${prefix}__mask.nii.gz
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

modules/local/mouse/brainextraction/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_bet"  

modules/local/mouse/brainextraction/main.nf

@@ -0,0 +1,37 @@
+process MOUSE_BRAINEXTRACTION {
+    tag "$meta.id"
+    label 'process_high'
+
+    container "scilus/antspynet:dev"
+
+    input:
+        tuple val(meta), path(anat)
+    output:
+        tuple val(meta), path("*__mask.nii.gz")      , emit: mask
+        path "versions.yml"                          , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+
+    """
+    antsMouseBrainExtraction $anat ${prefix}__mask.nii.gz
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsMouseBrainExtraction --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    """
+    antsMouseBrainExtraction -h
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        ants: \$(antsMouseBrainExtraction --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}

modules/local/mouse/brainextraction/meta.yml

@@ -0,0 +1,44 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "brainextraction"
+description: Extraction of the brain from anatomical images using BET
+keywords:
+  - BET
+  - T1
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+  - "FSL":
+      description: "FSL Toolbox and Scilpy Toolbox"
+      homepage: "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki"
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - anat:
+      type: file
+      description: Anat Nifti image
+      pattern: "*.{nii,nii.gz}"
+
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - mask:
+      type: file
+      description: mask brain-extracted
+      pattern: "*__mask.{nii,nii.gz}"
+
+
+authors:
+  - "@EliseCos"

modules/local/mouse/convertbet/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_convertbet"  

modules/local/mouse/convertbet/main.nf

@@ -0,0 +1,51 @@
+process MOUSE_CONVERTBET {
+    tag "$meta.id"
+    label 'process_low'
+
+    container "scilus/scilus:2.2.0"
+
+    input:
+        tuple val(meta), path(image)
+    output:
+        tuple val(meta), path("*_mask.nii.gz")                      , emit: mask
+        path "versions.yml"                                         , emit: versions
+
+    when:
+    task.ext.when == null || task.ext.when
+
+    script:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def nb_vox = task.ext.nb_vox ?: ""
+    """
+    fslmaths ${image} -bin ${prefix}_mask.nii.gz
+
+    scil_volume_math erosion ${prefix}_mask.nii.gz $nb_vox ${prefix}_mask.nii.gz --data_type uint8 -f
+    ImageMath 3 ${prefix}_mask.nii.gz  GetLargestComponent ${prefix}_mask.nii.gz 
+    scil_volume_math dilation ${prefix}_mask.nii.gz $nb_vox ${prefix}_mask.nii.gz --data_type uint8 -f
+    ImageMath 3 ${prefix}_mask.nii.gz  FillHoles ${prefix}_mask.nii.gz 
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+	    scilpy: \$(uv -q -n pip list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(ImageMath --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+
+    stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    """
+    fslmaths
+    scil_volume_math -h
+    ImageMath
+
+    touch ${prefix}_mask.nii.gz 
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        scilpy: \$(uv pip -q -n list | grep scilpy | tr -s ' ' | cut -d' ' -f2)
+        fsl: \$(flirt -version 2>&1 | sed -n 's/FLIRT version \\([0-9.]\\+\\)/\\1/p')
+        ants: \$(ImageMath --version 2>&1 | sed -n 's/ANTs Version: v\\([0-9.]\\+\\)/\\1/p')
+    END_VERSIONS
+    """
+}

modules/local/mouse/convertbet/meta.yml

@@ -0,0 +1,44 @@
+---
+# yaml-language-server: $schema=https://raw.githubusercontent.com/scilus/nf-neuro/main/modules/meta-schema.json
+name: "mouse_convertjson"
+description: Convert stats to JSON
+keywords:
+  - stats
+  - convert
+tools:
+  - "scilpy":
+      description: "The Sherbrooke Connectivity Imaging Lab (SCIL) Python dMRI processing toolbox."
+      homepage: "https://github.com/scilus/scilpy.git"
+input:
+  # Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - stats:
+      type: list
+      description: DWI Nifti image
+      pattern: "*.{nii,nii.gz}"
+
+output:
+  #Only when we have meta
+  - meta:
+      type: map
+      description: |
+        Groovy Map containing sample information
+        e.g. `[ id:'test', single_end:false ]`
+
+  - stats_json:
+      type: file
+      description: File with stats
+      pattern: "stats_reorganized.json"
+
+  - versions:
+      type: file
+      description: File containing software versions
+      pattern: "versions.yml"
+
+authors:
+  - "@EliseCos"

modules/local/mouse/convertjson/main.nf

@@ -25,6 +25,7 @@ process MOUSE_CONVERTJSON {
     """
 
     stub:
+    def prefix = task.ext.prefix ?: "${meta.id}"
     """
     touch ${prefix}__stats_reorganized.json
 

modules/local/mouse/preparebet/environment.yml

@@ -0,0 +1,3 @@
+channels: []
+dependencies: []
+name: "mouse_preparebet"