Updated tests for newly added tools

Author: KunaalAgarwal

public/cwl/amico/amico_noddi.cwl

@@ -1,26 +1,25 @@
 #!/usr/bin/env cwl-runner
 
-# https://github.com/daducci/AMICO
+# https://github.com/cookpa/amico-noddi
 # AMICO NODDI (Neurite Orientation Dispersion and Density Imaging) fitting
 # Uses convex optimization for fast and robust estimation of NODDI parameters
 
 cwlVersion: v1.2
 class: CommandLineTool
-baseCommand: ['python3', '-c']
 
 hints:
   DockerRequirement:
-    dockerPull: cookpa/amico-noddi:latest
+    dockerPull: cookpa/amico-noddi:0.1.2
 
 requirements:
   InitialWorkDirRequirement:
     listing:
       - entry: $(inputs.dwi)
         entryname: dwi.nii.gz
       - entry: $(inputs.bvals)
-        entryname: bvals
+        entryname: dwi.bval
       - entry: $(inputs.bvecs)
-        entryname: bvecs
+        entryname: dwi.bvec
       - entry: $(inputs.mask)
         entryname: mask.nii.gz
   InlineJavascriptRequirement: {}
@@ -29,18 +28,14 @@ stdout: amico_noddi.log
 stderr: amico_noddi.err.log
 
 arguments:
-  - position: 1
-    valueFrom: |
-      import amico
-      import os
-      amico.core.setup()
-      ae = amico.Evaluation('.', '.')
-      ae.load_data('dwi.nii.gz', 'bvals', 'bvecs', mask_filename='mask.nii.gz')
-      ae.set_model('NODDI')
-      ae.generate_kernels()
-      ae.load_kernels()
-      ae.fit()
-      ae.save_results()
+  - prefix: --dwi-root
+    valueFrom: dwi
+  - prefix: --brain-mask
+    valueFrom: mask.nii.gz
+  - prefix: --output-root
+    valueFrom: output/NODDI
+  - prefix: --work-dir
+    valueFrom: /tmp/amico_work
 
 inputs:
   dwi:
@@ -55,28 +50,51 @@ inputs:
   mask:
     type: File
     label: Brain mask image
+  num_threads:
+    type: ['null', int]
+    label: Maximum number of CPU threads (default 1)
+    inputBinding:
+      prefix: --num-threads
+  b0_threshold:
+    type: ['null', int]
+    label: Threshold for considering measurements b=0 (default 10)
+    inputBinding:
+      prefix: --b0-threshold
+  csf_diffusivity:
+    type: ['null', double]
+    label: CSF diffusivity in mm^2/s (default 0.003)
+    inputBinding:
+      prefix: --csf-diffusivity
+  parallel_diffusivity:
+    type: ['null', double]
+    label: Intracellular diffusivity parallel to neurites in mm^2/s (default 0.0017)
+    inputBinding:
+      prefix: --parallel-diffusivity
+  ex_vivo:
+    type: ['null', boolean]
+    label: Use ex-vivo AMICO model
+    inputBinding:
+      prefix: --ex-vivo
+      valueFrom: '$(self ? "1" : "0")'
 
 outputs:
   ndi_map:
     type: File
     outputBinding:
       glob:
-        - AMICO/NODDI/FIT_ICVF.nii.gz
-        - FIT_ICVF.nii.gz
+        - output/NODDI*ICVF.nii.gz
     label: Neurite Density Index (NDI/ICVF) map
   odi_map:
     type: File
     outputBinding:
       glob:
-        - AMICO/NODDI/FIT_OD.nii.gz
-        - FIT_OD.nii.gz
+        - output/NODDI*OD.nii.gz
     label: Orientation Dispersion Index (ODI) map
   fiso_map:
     type: File
     outputBinding:
       glob:
-        - AMICO/NODDI/FIT_ISOVF.nii.gz
-        - FIT_ISOVF.nii.gz
+        - output/NODDI*ISOVF.nii.gz
     label: Isotropic Volume Fraction (fISO) map
   log:
     type: File

public/cwl/fsl/applytopup.cwl

@@ -11,6 +11,15 @@ hints:
   DockerRequirement:
     dockerPull: brainlife/fsl:latest
 
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: $(inputs.topup_fieldcoef.basename)
+        entry: $(inputs.topup_fieldcoef)
+      - entryname: $(inputs.topup_movpar.basename)
+        entry: $(inputs.topup_movpar)
+
 stdout: applytopup.log
 stderr: applytopup.err.log
 
@@ -21,12 +30,12 @@ inputs:
     inputBinding:
       prefix: --imain=
       separate: false
-  topup_prefix:
-    type: string
-    label: Basename of the topup output (field coefficients)
-    inputBinding:
-      prefix: --topup=
-      separate: false
+  topup_fieldcoef:
+    type: File
+    label: Topup field coefficients file (_fieldcoef.nii.gz from topup)
+  topup_movpar:
+    type: File
+    label: Topup movement parameters file (_movpar.txt from topup)
   encoding_file:
     type: File
     label: Acquisition parameters file (same as used for topup)
@@ -79,6 +88,11 @@ inputs:
     inputBinding:
       prefix: -v
 
+arguments:
+  - prefix: --topup=
+    separate: false
+    valueFrom: $(inputs.topup_fieldcoef.basename.replace(/_fieldcoef\.nii\.gz$|_fieldcoef\.nii$/, ''))
+
 outputs:
   corrected_images:
     type: File

public/cwl/fsl/bianca.cwl

@@ -9,7 +9,14 @@ baseCommand: 'bianca'
 
 hints:
   DockerRequirement:
-    dockerPull: brainlife/fsl:latest
+    dockerPull: brainlife/fsl:6.0.4-patched2
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entry: $(inputs.training_data)
+        writable: false
 
 stdout: bianca.log
 stderr: bianca.err.log
@@ -21,6 +28,9 @@ inputs:
     inputBinding:
       prefix: --singlefile=
       separate: false
+  training_data:
+    type: Directory
+    label: Directory containing all subject data files referenced in master file
   querysubjectnum:
     type: int
     label: Row number in master file for the subject to segment

public/cwl/fsl/fsl_prepare_fieldmap.cwl

@@ -45,6 +45,7 @@ inputs:
     label: Suppress sanity checking of image size/range/dimensions
     inputBinding:
       prefix: --nocheck
+      position: 6
 
 outputs:
   fieldmap:

public/cwl/fsl/tbss_non_FA.cwl

@@ -20,6 +20,9 @@ requirements:
       - entry: $(inputs.stats_directory)
         entryname: stats
         writable: true
+      - entry: $(inputs.measure_directory)
+        entryname: $(inputs.measure)
+        writable: true
 
 stdout: tbss_non_FA.log
 stderr: tbss_non_FA.err.log
@@ -32,10 +35,13 @@ inputs:
       position: 1
   fa_directory:
     type: Directory
-    label: FA directory from TBSS pipeline
+    label: FA directory from TBSS pipeline (contains per-subject FA images and warps)
   stats_directory:
     type: Directory
-    label: stats directory containing all_<measure>.nii.gz
+    label: stats directory (mean_FA_skeleton, skeleton_mask, all_FA, all_FA_skeletonised)
+  measure_directory:
+    type: Directory
+    label: Directory containing per-subject non-FA images (filenames must match FA subjects without _FA suffix)
 
 outputs:
   skeletonised_data:

public/cwl/toolMap.js

@@ -4377,7 +4377,8 @@ export const TOOL_MAP = {
         requiredInputs: {
             measure: { type: 'string', label: 'Non-FA measure name (e.g., MD, AD, RD)' },
             fa_directory: { type: 'Directory', passthrough: true, label: 'FA directory from TBSS pipeline' },
-            stats_directory: { type: 'Directory', label: 'Stats directory containing all_<measure>.nii.gz' }
+            stats_directory: { type: 'Directory', label: 'Stats directory (mean_FA_skeleton, skeleton_mask, all_FA, all_FA_skeletonised)' },
+            measure_directory: { type: 'Directory', label: 'Directory with per-subject non-FA images (names matching FA subjects without _FA suffix)' }
         },
 
         optionalInputs: {},
@@ -4399,7 +4400,8 @@ export const TOOL_MAP = {
 
         requiredInputs: {
             input: { type: 'File', passthrough: true, label: 'Input image(s) to correct', acceptedExtensions: ['.nii', '.nii.gz'] },
-            topup_prefix: { type: 'string', label: 'Basename of topup output (field coefficients)' },
+            topup_fieldcoef: { type: 'File', label: 'Topup field coefficients file (_fieldcoef.nii.gz)', acceptedExtensions: ['.nii', '.nii.gz'] },
+            topup_movpar: { type: 'File', label: 'Topup movement parameters file (_movpar.txt)', acceptedExtensions: ['.txt'] },
             encoding_file: { type: 'File', label: 'Acquisition parameters file' },
             inindex: { type: 'string', label: 'Comma-separated indices into encoding file' },
             output: { type: 'string', label: 'Output basename for corrected images' }
@@ -4486,14 +4488,15 @@ export const TOOL_MAP = {
 
         requiredInputs: {
             singlefile: { type: 'File', passthrough: true, label: 'Master file listing subjects, images, masks, and transformations' },
+            training_data: { type: 'Directory', label: 'Directory containing all subject data files referenced in master file' },
             querysubjectnum: { type: 'int', label: 'Row number for subject to segment' },
             brainmaskfeaturenum: { type: 'int', label: 'Column number containing brain mask' },
             labelfeaturenum: { type: 'int', label: 'Column number containing manual lesion mask' },
-            trainingnums: { type: 'string', label: 'Training subject row numbers (comma-separated or "all")' },
-            output_name: { type: 'string', label: 'Output file basename' }
+            trainingnums: { type: 'string', label: 'Training subject row numbers (comma-separated or "all")' }
         },
 
         optionalInputs: {
+            output_name: { type: 'string', label: 'Output file basename (default: bianca_output)' },
             featuresubset: { type: 'string', label: 'Column numbers for intensity features (comma-separated)', flag: '--featuresubset' },
             matfeaturenum: { type: 'int', label: 'Column number containing MNI transformation matrices', flag: '--matfeaturenum' },
             spatialweight: { type: 'double', label: 'Weighting for MNI spatial coordinates (default 1)', flag: '--spatialweight' },
@@ -4732,12 +4735,18 @@ export const TOOL_MAP = {
             mask: { type: 'File', label: 'Brain mask image', acceptedExtensions: ['.nii', '.nii.gz'] }
         },
 
-        optionalInputs: {},
+        optionalInputs: {
+            num_threads: { type: 'int', label: 'Maximum number of CPU threads (default 1)' },
+            b0_threshold: { type: 'int', label: 'Threshold for considering measurements b=0 (default 10)' },
+            csf_diffusivity: { type: 'double', label: 'CSF diffusivity in mm^2/s (default 0.003)' },
+            parallel_diffusivity: { type: 'double', label: 'Intracellular diffusivity parallel to neurites in mm^2/s (default 0.0017)' },
+            ex_vivo: { type: 'boolean', label: 'Use ex-vivo AMICO model' }
+        },
 
         outputs: {
-            ndi_map: { type: 'File', label: 'Neurite Density Index (NDI/ICVF) map', glob: ['AMICO/NODDI/FIT_ICVF.nii.gz', 'FIT_ICVF.nii.gz'] },
-            odi_map: { type: 'File', label: 'Orientation Dispersion Index (ODI) map', glob: ['AMICO/NODDI/FIT_OD.nii.gz', 'FIT_OD.nii.gz'] },
-            fiso_map: { type: 'File', label: 'Isotropic Volume Fraction (fISO) map', glob: ['AMICO/NODDI/FIT_ISOVF.nii.gz', 'FIT_ISOVF.nii.gz'] },
+            ndi_map: { type: 'File', label: 'Neurite Density Index (NDI/ICVF) map', glob: ['output/NODDI*ICVF.nii.gz'] },
+            odi_map: { type: 'File', label: 'Orientation Dispersion Index (ODI) map', glob: ['output/NODDI*OD.nii.gz'] },
+            fiso_map: { type: 'File', label: 'Isotropic Volume Fraction (fISO) map', glob: ['output/NODDI*ISOVF.nii.gz'] },
             log: { type: 'File', label: 'Log file', glob: ['amico_noddi.log'] },
             err_log: { type: 'File', label: 'Error log file', glob: ['amico_noddi.err.log'] }
         }

utils/amico_tests/_common.sh

@@ -3,10 +3,10 @@
 # Source this file at the top of every test_*.sh script.
 
 # Chain to the structural MRI common infrastructure
-source "$(cd "$(dirname "${BASH_SOURCE[1]:-${BASH_SOURCE[0]}"}")/../structural_mri_tests" && pwd)/_common.sh"
+source "$(cd "$(dirname "${BASH_SOURCE[1]:-${BASH_SOURCE[0]}}")"/../structural_mri_tests && pwd)/_common.sh"
 
 # Docker image
-AMICO_IMAGE="${AMICO_DOCKER_IMAGE:-cookpa/amico-noddi:latest}"
+AMICO_IMAGE="${AMICO_DOCKER_IMAGE:-cookpa/amico-noddi:0.1.2}"
 
 docker_amico() {
   _docker_run "$AMICO_IMAGE" "$@"

utils/amico_tests/test_amico_noddi.sh

@@ -31,13 +31,13 @@ EOF
 run_tool "$TOOL" "${JOB_DIR}/${TOOL}.yml" "$CWL"
 
 # ── Verify outputs ─────────────────────────────────────────────
+# AMICO output naming uses 'x' separator: NODDIFITxICVF.nii.gz
 dir="${OUT_DIR}/${TOOL}"
-expected_outputs=("FIT_ICVF.nii.gz" "FIT_OD.nii.gz" "FIT_ISOVF.nii.gz")
+expected_patterns=("NODDI*ICVF.nii.gz" "NODDI*OD.nii.gz" "NODDI*ISOVF.nii.gz")
 
-for expected in "${expected_outputs[@]}"; do
-  # Check in both AMICO/NODDI/ subdirectory and top-level
+for pattern in "${expected_patterns[@]}"; do
   found_file=""
-  for candidate in "${dir}/AMICO/NODDI/${expected}" "${dir}/${expected}"; do
+  for candidate in "${dir}"/${pattern} "${dir}"/output/${pattern}; do
     if [[ -f "$candidate" ]]; then
       found_file="$candidate"
       break
@@ -48,8 +48,8 @@ for expected in "${expected_outputs[@]}"; do
     if [[ ! -s "$found_file" ]]; then
       echo "  FAIL: zero-byte output: $found_file"; exit 1
     fi
-    echo "  OK: ${expected} ($(wc -c < "$found_file") bytes)"
+    echo "  OK: $(basename "$found_file") ($(wc -c < "$found_file") bytes)"
   else
-    echo "  WARN: ${expected} not found"
+    echo "  WARN: ${pattern} not found"
   fi
 done