add stats invocation

cpp-lln-lab · Aug 6, 2024 · e478d80 · e478d80
1 parent 03bec6e
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diff --git a/boutiques/README.md b/boutiques/README.md
@@ -6,4 +6,9 @@ This directory contains a
 ## How to use
 
 * Install Boutiques: `pip install boutiques`
-* Run the example: `bosh exec launch --no-container  boutiques/bidspm_3.1.1.json boutiques/invocation.json`
+* Run the example:
+
+```bash
+bosh exec launch --no-container  boutiques/bidspm_3.1.1.json boutiques/invocation_smooth.json
+bosh exec launch --no-container  boutiques/bidspm_3.1.1.json boutiques/invocation_stats.json
+```
diff --git a/boutiques/bidspm_3.1.1.json b/boutiques/bidspm_3.1.1.json
@@ -380,7 +380,6 @@
           "ignore"
         ],
         "default_model": [
-          "space",
           "roi_based",
           "keep_residuals",
           "node_name",
@@ -393,22 +392,14 @@
           "models_dir",
           "fwhm",
           "boilerplate_only",
-          "task",
           "dry_run",
           "roi_name",
-          "participant_label",
           "roi_dir",
           "design_only",
           "use_dummy_regressor",
-          "skip_validation",
-          "anat_only",
-          "bids_filter_file",
-          "ignore",
-          "options",
-          "verbosity"
+          "anat_only"
         ],
         "create_roi": [
-          "space",
           "roi_based",
           "keep_residuals",
           "node_name",
@@ -420,92 +411,50 @@
           "boilerplate_only",
           "task",
           "dry_run",
-          "participant_label",
           "roi_dir",
           "design_only",
           "use_dummy_regressor",
           "skip_validation",
           "anat_only",
-          "bids_filter_file",
           "ignore",
-          "options",
           "verbosity"
         ],
         "stats": [
-          "space",
-          "preproc_dir",
           "hemisphere",
-          "roi_atlas",
           "dummy_scans",
           "models_dir",
-          "fwhm",
-          "boilerplate_only",
-          "task",
-          "dry_run",
-          "roi_name",
-          "participant_label",
-          "skip_validation",
-          "anat_only",
-          "bids_filter_file",
-          "ignore",
-          "options",
-          "verbosity"
+          "anat_only"
         ],
         "contrasts": [
-          "space",
           "roi_based",
           "keep_residuals",
-          "node_name",
-          "model_file",
-          "preproc_dir",
           "hemisphere",
           "roi_atlas",
-          "concatenate",
           "dummy_scans",
           "models_dir",
-          "fwhm",
-          "boilerplate_only",
-          "task",
-          "dry_run",
           "roi_name",
           "participant_label",
           "roi_dir",
           "design_only",
           "use_dummy_regressor",
           "skip_validation",
           "anat_only",
-          "bids_filter_file",
-          "ignore",
-          "options",
-          "verbosity"
+          "ignore"
         ],
         "results": [
-          "space",
           "roi_based",
           "keep_residuals",
           "node_name",
-          "model_file",
-          "preproc_dir",
           "hemisphere",
-          "roi_atlas",
           "concatenate",
           "dummy_scans",
           "models_dir",
-          "fwhm",
-          "boilerplate_only",
-          "task",
-          "dry_run",
           "roi_name",
-          "participant_label",
           "roi_dir",
           "design_only",
           "use_dummy_regressor",
-          "skip_validation",
           "anat_only",
-          "bids_filter_file",
-          "ignore",
-          "options",
-          "verbosity"
+          "ignore"
         ],
         "bms": [
           "space",
@@ -518,21 +467,14 @@
           "roi_atlas",
           "concatenate",
           "dummy_scans",
-          "fwhm",
           "boilerplate_only",
           "task",
-          "dry_run",
           "roi_name",
-          "participant_label",
           "roi_dir",
           "design_only",
           "use_dummy_regressor",
-          "skip_validation",
           "anat_only",
-          "bids_filter_file",
-          "ignore",
-          "options",
-          "verbosity"
+          "ignore"
         ]
       }
     }

diff --git a/boutiques/invocation.json → boutiques/invocation_smooth.json b/boutiques/invocation.json → boutiques/invocation_smooth.json
diff --git a/boutiques/invocation_stats.json b/boutiques/invocation_stats.json
@@ -0,0 +1,17 @@
+{
+  "bids_dir": "./demos/openneuro/inputs/ds000114",
+  "output_dir": "./demos/openneuro/outputs/ds000114/derivatives",
+  "analysis_level": "subject",
+  "command": "stats",
+  "participant_label": [
+    "01",
+    "02"
+  ],
+  "preproc_dir": "./demos/openneuro/outputs/ds000114/derivatives/bidspm-preproc",
+  "verbosity": 2,
+  "fwhm": 6.0,
+  "model_file": "./demos/openneuro/models/model-ds000114_desc-testRetestVerbal_smdl.json",
+  "dry_run": false,
+  "skip_validation": true,
+  "roi_atlas": "hcpex"
+}
diff --git a/demos/openneuro/ds000114_run.m b/demos/openneuro/ds000114_run.m
@@ -10,6 +10,7 @@
 
 SMOOTH = false;
 TASK = 'verbal'; % 'verbal' / 'linebisection'
+FWHM = 6;
 
 % The directory where the data are located
 root_dir = fileparts(mfilename('fullpath'));
@@ -50,7 +51,7 @@
          'action', 'smooth', ...
          'task', task, ...
          'space', space, ...
-         'fwhm', 8, ...
+         'fwhm', FWHM, ...
          'verbosity', 3); %#ok<*UNRCH>
 end
 
@@ -65,7 +66,7 @@
        'model_file', model_file, ...
        'roi_atlas', 'hcpex', ...
        'space', space, ...
-       'fwhm', 8, ...
+       'fwhm', FWHM, ...
        'skip_validation', true, ...
        'options', opt, ...
        'verbosity', 3);