Merge pull request #2 from frheault/update_scilpy

WIP - Adaptation to scilpy
scilus · Oct 23, 2020 · c0ba111 · c0ba111
2 parents aec0f54 + 2171c6f
commit c0ba111
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Showing 4 changed files with 26 additions and 17 deletions.
diff --git a/README.md b/README.md
@@ -2,6 +2,8 @@
 ===================
 
 Run the Bundle Specific Tractography pipeline.
+To access the template in the original publication:
+https://zenodo.org/record/4104309#.X4xduZ1KhdU
 
 If you use this pipeline, please cite:
 

diff --git a/USAGE b/USAGE
@@ -3,11 +3,11 @@ Pipeline for bundle-specific tractography
 
 USAGE
 
-nextflow run main.nf --root ... [OPTIONAL_ARGUMENTS]
+nextflow run main.nf --input ... [OPTIONAL_ARGUMENTS]
 
 DESCRIPTION
 
---root=/path/to/[root]              Root folder containing multiple subjects
+--input=/path/to/[root]              Root folder containing multiple subjects
 
                                     [root]
                                     ├── S1
@@ -40,7 +40,7 @@ OPTIONAL ARGUMENTS (current value)
 --seeding                               Seeding strategy, either npv or nts ($seeding)
 --nbr_seeds                             Number of seeds to initialize, per voxel or total ($nbr_seeds)
 --algo                                  Choice between "prob", "det" or "prob,det" ($algo)
---basis                                 SH basis of the input FOD ($basis)
+--sh_basis                              SH basis of the input FOD, descoteaux07 or tournier07 ($sh_basis)
 --min_length                            Minimal length in mm of streamline ($min_length)
 --max_length                            Maximal length in mm of streamline ($max_length)
 --compress_error_tolerance              Error tolerance for streamline compression in mm ($compress_error_tolerance)

diff --git a/main.nf b/main.nf
@@ -16,7 +16,7 @@ if(params.help) {
                 "seeding":"$params.seeding",
                 "nbr_seeds":"$params.nbr_seeds",
                 "algo":"$params.algo",
-                "basis":"$params.basis",
+                "sh_basis":"$params.sh_basis",
                 "min_length":"$params.min_length",
                 "max_length":"$params.max_length",
                 "compress_error_tolerance":"$params.compress_error_tolerance",
@@ -81,8 +81,8 @@ log.info "Outlier Removal Alpha: $params.outlier_alpha"
 log.info ""
 log.info ""
 
-log.info "Input: $params.root"
-root = file(params.root)
+log.info "Input: $params.input"
+root = file(params.input)
 /* Watch out, files are ordered alphabetically in channel */
     in_data = Channel
         .fromFilePairs("$root/**/{*fa.nii.gz,*fodf.nii.gz,*tracking_mask.nii.gz}",
@@ -96,6 +96,11 @@ root = file(params.root)
                         maxDepth:2,
                         flat: true) {it.parent.name}
 
+if (!(params.atlas_anat) || !(params.atlas_directory)) {
+    error "You must specify all 2 atlas related input. --atlas_anat " +
+    "and --atlas_directory all are mandatory."
+}
+
     atlas_anat = Channel.fromPath("$params.atlas_anat")
     atlas_bundles = Channel.fromPath("$params.atlas_directory/*.trk")
     algo_list = params.algo?.tokenize(',')
@@ -130,6 +135,7 @@ process Register_Anat {
     output:
     set sid, "${sid}__output1InverseWarp.nii.gz", "${sid}__output0GenericAffine.mat" into deformation_for_warping
     file "${sid}__outputWarped.nii.gz"
+    file "${sid}__output1Warp.nii.gz"
     script:
     """
     antsRegistrationSyNQuick.sh -d 3 -f ${native_anat} -m ${atlas} -n ${params.register_processes} -o ${sid}__output
@@ -150,9 +156,7 @@ process Warp_Bundle {
     set sid, val(bundle_name.baseName), "${sid}__${bundle_name.baseName}_warp.trk" into bundles_for_priors, models_for_recobundles
     script:
     """
-    ConvertTransformFile 3 ${affine} ${affine}.txt --hm --ras
-    scil_apply_transform_to_tractogram.py ${bundle_name} ${warp} ${affine}.txt ${bundle_name.baseName}_linear.trk --inverse --remove_invalid -f
-    scil_apply_warp_to_tractogram.py ${bundle_name.baseName}_linear.trk ${anat} ${warp} ${sid}__${bundle_name.baseName}_warp.trk --remove_invalid -f
+    scil_apply_transform_to_tractogram.py ${bundle_name} ${anat} ${affine} ${sid}__${bundle_name.baseName}_warp.trk --inverse --cut_invalid --in_deformation ${warp}
     """ 
 }
 
@@ -179,8 +183,9 @@ process Generate_Priors {
     set sid, val(bundle_name), "${sid}__${bundle_name}_endpoints_mask_dilate.nii.gz" into masks_for_map_in
     script:
     """
-    scil_generate_priors_from_bundle.py ${bundle} ${fod} ${mask} \
-        --sh_basis $params.basis --output_prefix ${sid}__${bundle_name}_
+    scil_image_math.py convert ${mask} mask.nii.gz --data_type uint8
+    scil_generate_priors_from_bundle.py ${bundle} ${fod} mask.nii.gz \
+        --sh_basis $params.sh_basis --out_prefix ${sid}__${bundle_name}_
     scil_image_math.py dilation ${sid}__${bundle_name}_todi_mask.nii.gz \
         $params.bs_tracking_mask_dilation dilate_todi.nii.gz --data_type uint8
     scil_image_math.py multiplication ${mask} dilate_todi.nii.gz \
@@ -226,11 +231,11 @@ process Tracking_Mask {
     script:
     if (params.use_bs_tracking_mask)
         """
-        mv ${bs_mask} ${sid}__${bundle_name}_tracking_mask.nii.gz
+        scil_image_math.py convert ${bs_mask} ${sid}__${bundle_name}_tracking_mask.nii.gz --data_type uint8
         """
     else
         """
-        mv ${tracking_mask} ${sid}__${bundle_name}_tracking_mask.nii.gz
+        scil_image_math.py convert ${tracking_mask} ${sid}__${bundle_name}_tracking_mask.nii.gz --data_type uint8
         """
 }
 
@@ -260,10 +265,12 @@ process Local_Tracking {
     script:
     """
     scil_compute_local_tracking.py ${efod} ${seeding_mask} ${tracking_mask} \
-        ${sid}__${bundle_name}_${algo}_${params.seeding}_${params.nbr_seeds}.trk \
-        --sh_basis $params.basis --min_len $params.min_length --max_len $params.max_length \
+        tracking.trk --sh_basis $params.sh_basis --min_len $params.min_length --max_len $params.max_length \
         --$params.seeding $params.nbr_seeds --compress $params.compress_error_tolerance \
         --seed $params.tracking_seed --algo ${algo}
+    scil_remove_invalid_streamlines.py tracking.trk tracking_ic.trk
+    scil_filter_tractogram.py tracking_ic.trk ${sid}__${bundle_name}_${algo}_${params.seeding}_${params.nbr_seeds}.trk \
+        --drawn_roi ${seeding_mask} either_end include
     """
 }
 
@@ -344,7 +351,7 @@ process PFT_Tracking {
     """
     scil_compute_pft.py ${efod} ${seeding_mask} ${map_include} ${map_exclude} \
         ${sid}__${bundle_name}_${algo}_${params.seeding}_${params.nbr_seeds}.trk \
-        --algo $algo --sh_basis $params.basis --min_length $params.min_length \
+        --algo $algo --sh_basis $params.sh_basis --min_length $params.min_length \
         --max_length $params.max_length --$seeding $params.nbr_seeds \
         --compress $params.compress_error_tolerance --seed $params.tracking_seed
     scil_remove_invalid_streamlines.py ${sid}__${bundle_name}_${algo}_${params.seeding}_${params.nbr_seeds}.trk  ${sid}__${bundle_name}_${algo}_${params.seeding}_${params.nbr_seeds}.trk -f

diff --git a/nextflow.config b/nextflow.config
@@ -26,7 +26,7 @@ params {
     seeding="npv"
     nbr_seeds=1
     algo="prob"
-    basis="descoteaux07"
+    sh_basis="descoteaux07"
     min_length=20
     max_length=200
     compress_error_tolerance=0.2