diff --git a/boutiques/README.md b/boutiques/README.md index 058a654a..becc0c22 100644 --- 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 index 8db73670..5f3156f2 100644 --- 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", @@ -420,53 +411,27 @@ "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", @@ -474,38 +439,22 @@ "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 b/boutiques/invocation_smooth.json similarity index 100% rename from boutiques/invocation.json rename to boutiques/invocation_smooth.json diff --git a/boutiques/invocation_stats.json b/boutiques/invocation_stats.json new file mode 100644 index 00000000..e3c1fdb2 --- /dev/null +++ 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 index 6f9df24b..98c4040a 100644 --- 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);