fix qc on tractogram when commit is run

scilus · Dec 31, 2024 · d91c36d · d91c36d
1 parent 4c5e87e
commit d91c36d
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Showing 6 changed files with 35 additions and 30 deletions.
diff --git a/conf/modules.config b/conf/modules.config
@@ -722,7 +722,6 @@ process {
             saveAs: {
                 filename ->
                 if ( filename.contains("commit.h5") ) { "${meta.id}_space-orig_desc-filtered_tracking.h5" }
-                else if ( filename.contains("commit.trk") ) { "${meta.id}_space-orig_desc-filtered_tracking.trk" }
                 else if ( filename.contains("versions.yml") ) { null }
                 else { params.lean_output ? null : filename }
             }

diff --git a/modules/local/filtering/commit.nf b/modules/local/filtering/commit.nf
@@ -7,11 +7,12 @@ process FILTERING_COMMIT {
         'scilus/scilpy:1.6.0' }"
 
     input:
-    tuple val(meta), path(trk), path(dwi), path(bval), path(bvec), path(peaks)
+    tuple val(meta), path(hdf5), path(dwi), path(bval), path(bvec), path(peaks)
 
     output:
     tuple val(meta), path("*results_bzs")   , emit: results
-    tuple val(meta), path("*commit*")       , emit: trk
+    tuple val(meta), path("*commit*")       , emit: hdf5
+    tuple val(meta), path("*essential*")    , emit: trk
 
     path "versions.yml"           , emit: versions
 
@@ -34,16 +35,20 @@ process FILTERING_COMMIT {
     """
     export DIPY_HOME="./"
 
-    scil_run_commit.py $trk $dwi $bval $bvec "${prefix}__results_bzs/" \
+    scil_run_commit.py $hdf5 $dwi $bval $bvec "${prefix}__results_bzs/" \
         --processes $task.cpus $para_diff $iso_diff $perp_diff $ball_stick \
         $commit2 $commit2_lambda $nbr_dir $peaks_arg
 
     if [ -f "${prefix}__results_bzs/commit_2/decompose_commit.h5" ]; then
         mv "${prefix}__results_bzs/commit_2/decompose_commit.h5" "./${prefix}__decompose_commit.h5"
-    elif [ -f "${prefix}__results_bzs/commit_1/decompose_commit.h5" ]; then
+    else
         mv "${prefix}__results_bzs/commit_1/decompose_commit.h5" "./${prefix}__decompose_commit.h5"
+    fi
+
+    if [ -f "${prefix}__results_bzs/commit_2/essential_tractogram.trk" ]; then
+        mv "${prefix}__results_bzs/commit_2/essential_tractogram.trk" "./${prefix}__essential.trk"
     else
-        mv "${prefix}__results_bzs/commit_1/essential_tractogram.trk" "./${prefix}__commit.trk"
+        mv "${prefix}__results_bzs/commit_1/essential_tractogram.trk" "./${prefix}__essential.trk"
     fi
 
     cat <<-END_VERSIONS > versions.yml
@@ -56,7 +61,8 @@ process FILTERING_COMMIT {
     def prefix = task.ext.prefix ?: "${meta.id}"
 
     """
-    touch ${prefix}__commit.trk
+    touch ${prefix}__commit.h5
+    touch ${prefix}__essential.trk
     mkdir ${prefix}__results_bzs
 
     scil_run_commit.py -h

diff --git a/tests/chained.nf.test.snap b/tests/chained.nf.test.snap
@@ -92,7 +92,7 @@
                 "sub-test/dwi/sub-test_space-orig_afd_sum.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_afd_total.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-brain_mask.nii.gz",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-pft_tracking.trk",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_dwi.bval",
@@ -125,7 +125,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:34:55.150076"
+        "timestamp": "2024-12-31T14:57:08.127054"
     },
     "Connectomics + tracking + infant profiles - should run successfully": {
         "content": [
@@ -222,7 +222,7 @@
                 "sub-test/dwi/sub-test_space-orig_afd_sum.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_afd_total.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-brain_mask.nii.gz",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_dwi.bval",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_dwi.bvec",
@@ -254,7 +254,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:37:53.688618"
+        "timestamp": "2024-12-31T14:59:22.789945"
     },
     "Connectomics + tracking + freesurfer profiles - should run successfully": {
         "content": [
@@ -365,7 +365,7 @@
                 "sub-test/dwi/sub-test_space-orig_afd_sum.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_afd_total.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-brain_mask.nii.gz",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-pft_tracking.trk",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_dwi.bval",
@@ -399,7 +399,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:31:53.502697"
+        "timestamp": "2024-12-31T14:55:00.755966"
     },
     "Freesurfer + connectomics profiles - should run successfully": {
         "content": [
@@ -466,7 +466,7 @@
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-sc.npy.png",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy.png",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_tracking.h5",
                 "sub-test/figures",
                 "sub-test/figures/sub-test_gradients_mqc.png",
@@ -482,7 +482,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:25:40.348832"
+        "timestamp": "2024-12-31T14:50:38.998744"
     },
     "Connectomics + tracking profiles - should run successfully": {
         "content": [
@@ -577,7 +577,7 @@
                 "sub-test/dwi/sub-test_space-orig_afd_sum.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_afd_total.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-brain_mask.nii.gz",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-pft_tracking.trk",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_dwi.bval",
@@ -610,6 +610,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:29:03.36884"
+        "timestamp": "2024-12-31T14:52:59.152676"
     }
 }
diff --git a/tests/connectomics.nf.test.snap b/tests/connectomics.nf.test.snap
@@ -42,7 +42,7 @@
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-sc.npy.png",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy.png",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_tracking.h5",
                 "sub-test/figures",
                 "sub-test/figures/sub-test_gradients_mqc.png",
@@ -57,7 +57,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:39:03.087726"
+        "timestamp": "2024-12-31T15:00:17.631141"
     },
     "Connectomics profile without metrics - should run successfully": {
         "content": [
@@ -102,7 +102,7 @@
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-sc.npy.png",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy.png",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_tracking.h5",
                 "sub-test/figures",
                 "sub-test/figures/sub-test_gradients_mqc.png",
@@ -117,7 +117,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:40:13.184442"
+        "timestamp": "2024-12-31T15:01:10.020385"
     },
     "Connectomics + infant profile - should run successfully": {
         "content": [
@@ -162,7 +162,7 @@
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-sc.npy.png",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy",
                 "sub-test/dwi/sub-test_ses-baseline_space-diff_seg-BrainnetomeChild_stat-vol.npy.png",
-                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.trk",
+                "sub-test/dwi/sub-test_space-orig_desc-filtered_tracking.h5",
                 "sub-test/dwi/sub-test_space-orig_desc-preproc_tracking.h5",
                 "sub-test/figures",
                 "sub-test/figures/sub-test_gradients_mqc.png",
@@ -177,6 +177,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:41:33.168064"
+        "timestamp": "2024-12-31T15:02:18.585569"
     }
 }
diff --git a/tests/multisubjects.nf.test.snap b/tests/multisubjects.nf.test.snap
@@ -94,7 +94,7 @@
                 "sub-test1/dwi/sub-test1_space-orig_afd_sum.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_afd_total.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_desc-brain_mask.nii.gz",
-                "sub-test1/dwi/sub-test1_space-orig_desc-filtered_tracking.trk",
+                "sub-test1/dwi/sub-test1_space-orig_desc-filtered_tracking.h5",
                 "sub-test1/dwi/sub-test1_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_desc-preproc_dwi.bval",
                 "sub-test1/dwi/sub-test1_space-orig_desc-preproc_dwi.bvec",
@@ -144,7 +144,7 @@
                 "sub-test2/dwi/sub-test2_space-orig_afd_sum.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_afd_total.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_desc-brain_mask.nii.gz",
-                "sub-test2/dwi/sub-test2_space-orig_desc-filtered_tracking.trk",
+                "sub-test2/dwi/sub-test2_space-orig_desc-filtered_tracking.h5",
                 "sub-test2/dwi/sub-test2_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_desc-preproc_dwi.bval",
                 "sub-test2/dwi/sub-test2_space-orig_desc-preproc_dwi.bvec",
@@ -176,7 +176,7 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:49:14.05649"
+        "timestamp": "2024-12-31T15:09:07.167014"
     },
     "All profiles with multiple subjects - should run successfully": {
         "content": [
@@ -287,7 +287,7 @@
                 "sub-test1/dwi/sub-test1_space-orig_afd_sum.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_afd_total.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_desc-brain_mask.nii.gz",
-                "sub-test1/dwi/sub-test1_space-orig_desc-filtered_tracking.trk",
+                "sub-test1/dwi/sub-test1_space-orig_desc-filtered_tracking.h5",
                 "sub-test1/dwi/sub-test1_space-orig_desc-pft_tracking.trk",
                 "sub-test1/dwi/sub-test1_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test1/dwi/sub-test1_space-orig_desc-preproc_dwi.bval",
@@ -355,7 +355,7 @@
                 "sub-test2/dwi/sub-test2_space-orig_afd_sum.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_afd_total.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_desc-brain_mask.nii.gz",
-                "sub-test2/dwi/sub-test2_space-orig_desc-filtered_tracking.trk",
+                "sub-test2/dwi/sub-test2_space-orig_desc-filtered_tracking.h5",
                 "sub-test2/dwi/sub-test2_space-orig_desc-pft_tracking.trk",
                 "sub-test2/dwi/sub-test2_space-orig_desc-preproc_b0.nii.gz",
                 "sub-test2/dwi/sub-test2_space-orig_desc-preproc_dwi.bval",
@@ -389,6 +389,6 @@
             "nf-test": "0.9.2",
             "nextflow": "24.10.1"
         },
-        "timestamp": "2024-12-30T12:46:00.157441"
+        "timestamp": "2024-12-31T15:06:13.046546"
     }
 }
diff --git a/workflows/pediatric.nf b/workflows/pediatric.nf
@@ -513,7 +513,7 @@ workflow PEDIATRIC {
         //
         // MODULE: Run AFDFIXEL
         //
-        ch_afdfixel = FILTERING_COMMIT.out.trk
+        ch_afdfixel = FILTERING_COMMIT.out.hdf5
             .join(ch_fodf)
 
         CONNECTIVITY_AFDFIXEL ( ch_afdfixel )