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manifest.json
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manifest.json
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{
"author": "Intermountain Neuroimaging Consortium",
"cite": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT#Referencing",
"command": "python /flywheel/v0/run.py",
"config": {
"task-list": {
"description": "Comma seperated list of tasks may be selected for FEAT 1st level analysis. Task name must be consistent with naming used in preprocessing package (e.g task-abc_run-01, task-abc_run-02). Regular expressions can also be used.",
"type": "string"
},
"events-suffix": {
"optional": true,
"description": "suffix used to select correct events file from bids curated dataset. Events may be pulled directly from acquisition container if no event file is passed as input.",
"type": "string"
},
"output-name": {
"optional": true,
"description": "[NAME].feat directory name. If left blank, output name will be drawn from the fsf template file.",
"type": "string"
},
"confound-list": {
"optional": true,
"type":"string",
"description": "Comma seperated list of components to be included in feat glm confounds. Confound timeseries will be pulled from confound file in inputs if passed, otherwise defaults to using bids derivative file '*counfound_timeseries.tsv'. Example entry: rot_x, rot_y, rot_z, trans_x, trans_y, trans_z. If left blank no confounds will be included in feat analysis."
},
"DropNonSteadyState": {
"type": "boolean",
"default": false,
"description": "set whether or not to remove XX number of inital non-steady state volumes. If no value is passed in 'DummyVolumes', non-steady state number is taken from mriqc IQMs, if neither are defined, an error will be returned."
},
"DummyVolumes": {
"type": "integer",
"optional": true,
"minimum": 0,
"maximum": 9999,
"description": "Number of dummy volumes to ignore at the beginning of scan. Leave blank if you want to use the non-steady state volumes recorded in mriqc IQMs."
},
"DropNonSteadyStateMethod": {
"default": "regressor",
"description": "(regressor | trim) Select method used to handle non-steady state volume removal. Warning: running concatenated 'multirun' option will always use trim removal method. Not relevant for higher level analysis. ",
"type": "string",
"enum": [
"regressor",
"trim"
]
},
"multirun": {
"type": "boolean",
"default": false,
"description": "select to concatenate all tasks in 'task-list' before running feat analysis. Otherwise each run will be run independently."
},
"evformat": {
"default": "BIDS-Formatted",
"description": "Select type of explanatory variable. Selected format should match format provided in the events input file, or files downloaded directly from flywheel acquisition. Options: BIDS-Formatted|FSL-3 Column Format|FSL-1 Entry Per Volume.",
"type": "string",
"enum": [
"BIDS-Formatted",
"FSL-3 Column Format",
"FSL-1 Entry Per Volume"
]
},
"allow-missing-evs": {
"type": "boolean",
"default": false,
"description": "Set to true to replace missing evs from template fsf with empty (zeros) regressor instead of exiting with error. Only select this option if you are confident the naming convention for events matches the fsf template."
},
"run-level": {
"default": "First Level Analysis",
"description": "Select appropriate run level (First Level Analysis | Higher Level Analysis). Higher level analysis skips certain design criteria specific for first level analysis setup.",
"type": "string",
"enum": [
"First Level Analysis",
"Higher Level Analysis"
]
},
"gear-log-level": {
"default": "INFO",
"description": "Gear Log verbosity level (ERROR|WARNING|INFO|DEBUG)",
"type": "string",
"enum": [
"ERROR",
"WARNING",
"INFO",
"DEBUG"
]
},
"gear-dry-run": {
"default": false,
"description": "Do everything except actually executing gear",
"type": "boolean"
},
"gear-writable-dir": {
"default": "/pl/active/ics/fw_temp_data",
"description": "Gears expect to be able to write temporary files in /flywheel/v0/. If this location is not writable (such as when running in Singularity), this path will be used instead. fMRIPrep creates a large number of files so this disk space should be fast and local.",
"type": "string"
},
"slurm-cpu": {
"default": "2",
"description": "[SLURM] How many cpu-cores to request per command/task. This is used for the underlying '--cpus-per-task' option. If not running on HPC, then this flag is ignored",
"type": "string"
},
"slurm-ram": {
"default": "16G",
"description": "[SLURM] How much RAM to request. This is used for the underlying '--mem-per-cpu' option. If not running on HPC, then this flag is ignored",
"type": "string"
},
"slurm-ntasks": {
"default": "1",
"description": "[SLURM] Total number of tasks/commands across all nodes (not equivalent to neuroimaging tasks). Using a value greater than 1 for code that has not been parallelized will not improve performance (and may break things).",
"type": "string"
},
"slurm-nodes": {
"default": "1",
"description": "[SLURM] How many HPC nodes to run on",
"type": "string"
},
"slurm-partition": {
"default": "blanca-ics",
"description": "[SLURM] Blanca, Alpine, or Summit partitions can be entered",
"type": "string"
},
"slurm-qos": {
"default": "blanca-ics",
"description": "[SLURM] For Blanca the QOS has a different meaning, ie blanca-ics vs blanca-ibg, etc. For Alpine and Summit, the QOS should be set to normal if running a job for 1 day or less, and set to long if running a job with a maximum walltime of 7 days",
"type": "string"
},
"slurm-account": {
"default": "blanca-ics",
"description": "[SLURM] For Blanca the ACCOUNT should be set to the sub-account of choice (e.g. blanca-ics-rray). For Alpine, the account should be set to ucb-general, or the specialized account granted by RC: ucb278_asc1",
"type": "string"
},
"slurm-time": {
"default": "1428",
"description": "[SLURM] Maximum walltime requested after which your job will be cancelled if it hasn't finished. Default to 1 day",
"type": "string"
}
},
"custom": {
"flywheel": {
"classification": [
"fMRI"
],
"components": [
"FSL"
],
"modality": [
"MR"
],
"suite": "Computational Models (GLM, etc)",
"type": [
"NIFTI"
]
},
"gear-builder": {
"category": "analysis",
"image": "amhe4269/bids-feat:6.0.4_inc0.8.2"
},
"license": "Apache-2.0"
},
"description": "(HPC Compatible) FSL's FEAT (FMRI Expert Analysis Tool). As implemented in this Gear, FEAT first level analysis will act on any generic bids compliant pipeline outputs. Voxelwise activation analyses for a single (or multiple) task will be generated. A template FSF design file is required, and all processing steps indicated in the design file will be followed.",
"environment": {
"FSF_OUTPUT_FORMAT": "nii.gz",
"FSLDIR": "/opt/fsl-6.0.4",
"USER": "flywheel",
"FSLMULTIFILEQUIT": "TRUE",
"FSLOUTPUTTYPE": "NIFTI_GZ",
"FSLTCLSH": "/opt/fsl-6.0.4/bin/fsltclsh",
"FSLWISH": "/opt/fsl-6.0.4/bin/fslwish",
"FSL_PYTHON": "${FSLDIR}/fslpython/envs/fslpython",
"LD_LIBRARY_PATH": "/usr/share/fsl/lib:/usr/share/fsl/lib",
"PATH": "/opt/poetry/bin:/opt/venv/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/opt/fsl-6.0.4/bin",
"REQUESTS_CA_BUNDLE": "/etc/ssl/certs/ca-certificates.crt",
"python3": "/opt/venv/bin/python3",
"python": "/opt/venv/bin/python",
"FLYWHEEL": "/flywheel/v0",
"POETRY_HOME": "/opt/poetry",
"POETRY_VERSION": "1.1.13",
"POETRY_VIRTUALENVS_CREATE": "false"
},
"inputs": {
"api-key": {
"base": "api-key"
},
"preprocessing-pipeline-zip": {
"description": "Select preprocessing output directory zip. Preprocessing outputs must be in bids derivative format. Example compatible pipelines: fmriprep, hcppipeline",
"base": "file",
"optional": true
},
"additional-input-one": {
"description": "(Optional) Additional preprocessing output directory. Preprocessing outputs must be in bids derivative format. ",
"base": "file",
"optional": true
},
"confounds-file": {
"description": "(Optional) Additional input used as confound timeseries in FSL FEAT. If no input is passed, default confounds file is used from bids derivative directory '*counfound_timeseries.tsv'.",
"base": "file",
"optional": true
},
"event-file": {
"base": "file",
"description": "Explanatory variable (EVs) custom text files. Identify in config options the event files type (BIDS-Formatted|FSL-3 Column Format|FSL-1 Entry Per Volume). If not event file is passed, events will be downloaded from flywheel acquisition.",
"optional": true
},
"FSF_TEMPLATE" : {
"base": "file",
"optional": false,
"description": "FSL DESIGN FILE that will be used as the template for all analyses. Record all common processing decisions in this file, for example slice-timing correction, intensity normization, EV naming and design. ",
"type": {
"enum": [
"text"
]
}
}
},
"label": "BIDS FSL: FEAT - fMRI preprocessing (v6.0)",
"license": "MIT",
"maintainer": "Amy Hegarty <amhe4260@colorado.edu>",
"name": "bids-feat",
"source": "https://github.com/intermountainneuroimaging/bids-feat",
"url": "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT",
"version": "6.0.4_inc0.8.2"
}