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MRIQC MPN for group analysis #8

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18bb936
mriqc mpn for group analysis
MontrealSergiy May 8, 2026
a931978
correct output template
MontrealSergiy May 8, 2026
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187 changes: 187 additions & 0 deletions boutiques_descriptors/mriqc_mpn_group_24_2_0.json
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{
"name": "MRIQC_MPN_GROUP",
"description": "MRIQC group analysis only. MRIQC extracts no-reference IQMs (image quality metrics) from structural (T1w and T2w) and functional MRI (magnetic resonance imaging) data. With additional features added within MPN project, such as support for T2starw and FLAIR modalities.",
"author": "The Poldrack lab (original MRIQC), Alex Pastor Bernier (enhancements)",
"tool-version": "24.2.0",
"schema-version": "0.5",
"command-line": "true [DERIVATIVES_PREFIX] [PARTICIPANT_RESULTS]; mkdir -p CB_DS; echo '{\"Name\": \"Example dataset\", \"BIDSVersion\": \"1.0.2\"}' > CB_DS/dataset_description.json && mriqc [SUBJECT_DIR] [PARTICIPANT_RESULTS] [GOUTPUT_DIR] group [BIDS_FILTER_FILE] --no-sub --n_cpus 1 -w work/.cb_mriqc_work [SESSION_ID] [RUN_ID] [TASK_ID] [MODALITIES]",
"inputs": [
{
"description": "Subject folders for BIDS (folders name should be sub-XXXXX).",
"id": "subject_dir",
"name": "Subject Directory",
"optional": false,
"list": true,
"type": "File",
"value-key": "[SUBJECT_DIR]"
},
{
"description": "Participant level analysis results.",
"id": "participant_results",
"name": "MRIQC Participant Analysis Results. Derivatives only.",
"optional": false,
"type": "File",
"list": true,
"value-key": "[PARTICIPANT_RESULTS]"
},
{
"command-line-flag": "--goutput_dir",
"description": "Group reports.",
"id": "group_results",
"name": "Tool output with MRIQC Group Analysis Results",
"optional": false,
"type": "String",
"value-key": "[GOUTPUT_DIR]"
},
{
"command-line-flag": "--session-id",
"id": "session_id",
"name": "Session ID",
"description": "filter input dataset by session id",
"optional": true,
"list": true,
"list-separator": " ",
"type": "String",
"value-key": "[SESSION_ID]"
},
{
"command-line-flag": "--run-id",
"id": "run_id",
"name": "Run ID",
"description": "filter input dataset by run id (only integer run ids are valid)",
"optional": true,
"list": true,
"list-separator": " ",
"type": "String",
"value-key": "[RUN_ID]"
},
{
"command-line-flag": "--task-id",
"id": "task_id",
"name": "Task ID",
"description": "filter input dataset by task id",
"optional": true,
"list": true,
"list-separator": " ",
"type": "String",
"value-key": "[TASK_ID]"
},
{
"command-line-flag": "--modalities",
"id": "modalities",
"name": "Modalities",
"description": "filter input dataset by MRI type",
"optional": true,
"list": true,
"list-separator": " ",
"type": "String",
"value-key": "[MODALITIES]",
"value-choices": [
"T1w",
"T2w",
"dwi",
"bold",
"T2starw",
"FLAIR"
]
},
{
"command-line-flag": "--bids-filter-file",
"description": "A JSON file describing custom BIDS input filters using PyBIDS.",
"id": "bids_filter_file",
"name": "BIDS Filter File",
"optional": true,
"type": "File",
"value-key": "[BIDS_FILTER_FILE]"
},
{
"default-value": "derivatives/",
"id": "derivatives_prefix",
"name": "derivatives_prefix",
"description": "Folders to put before the pipeline specific folder. By default this will look like DataProvider/derivatives/PipelineName, where pipeline name is specific to the current pipeline. The provided string must end in /. Experimental need specially configured dataprovider",
"optional": true,
"type": "String",
"value-key": "[DERIVATIVES_PREFIX]"
}
],
"output-files": [
{
"id": "output_dir",
"name": "Output Directory",
"description": "This is the output with group level reports.",
"path-template": "[GOUTPUT_DIR]",
"optional": false
}
],
"groups": [
{
"id": "non_standard_params",
"name": "Non-standard parameters",
"members": [
"modalities",
"task_id",
"run_id"
]
}
],
"tags": {
"application-type": [
"bids"
],
"domain": [
"neuroinformatics",
"mri",
"fmri",
"quality"
]
},
"suggested-resources": {
"cpu-cores": 1,
"ram": 4,
"walltime-estimate": 4400
},
"custom": {
"cbrain:readonly-input-files": true,
"cbrain:author": "Erik Lee <leex6144@umn.edu>, Serge Boroday <serge.boroday@mcin.ca>",
"cbrain:allow_empty_strings": [
"derivatives_prefix"
],
"cbrain:override-input-string-ruby-regex": {
"derivatives_prefix": ":relative-path:"
},
"cbrain:integrator_modules": {
"BoutiquesFileTypeVerifier": {
"subject_dir": [
"BidsSubject"
],
"participant_results": [
"MRIQCOutput"
],
"bids_filter_file": [
"JsonFile", "TextFile", "SingleFile"
]
},
"BoutiquesFileNameMatcher": {
"subject_dir": "^sub-[a-zA-Z0-9_]+$",
"participant_results": "/^(?!sub-[a-zA-Z0-9]{1,8}$).+$/"
},
"BoutiquesOutputFileTypeSetter": {
"output_dir": "FileCollection"
},
"BoutiquesForcedOutputBrowsePath": {
"output_dir": "[DERIVATIVES_PREFIX]mriqc"
},

"BoutiquesInputSubdirMaker": {
"participant_results": {
"dirname": "CB_MRIQC",
"append_filename": false
},
"subject_dir": {
"dirname": "CB_DS",
"append_filename": false
}
}
}
}
}