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manifest.json
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{
"name": "antsct-fw",
"label": "ANTs Cortical Thickness",
"description": "Gear version of the antsCorticalThickness.sh pipeline. Performs 1. Brain extraction 2. Brain n-tissue segmentation 3. Cortical thickness 4. (Optional) registration to a template",
"version": "0.4.0_0.2.0",
"inputs": {
"api_key": {
"base": "api-key"
},
"t1_anatomy": {
"description": "T1-weighted anatomical NIfTI file. When provided this file will be used in place of any T1w images found in the current session's BIDS dataset.",
"base": "file",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"template-zip": {
"base": "file",
"description": "zip file containing a template in template-flow format",
"optional": true
},
"mni-labels-1": {
"base": "file",
"description": "One or more generic label images in the MNI152NLin2009cAsym space, to be warped to the subject space.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"mni-labels-2": {
"base": "file",
"description": "One or more generic label images in the MNI152NLin2009cAsym space, to be warped to the subject space.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"mni-labels-3": {
"base": "file",
"description": "One or more generic label images in the MNI152NLin2009cAsym space, to be warped to the subject space.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"mni-cortical-labels-1": {
"base": "file",
"description": " One or more cortical label images in the MNI152NLin2009cAsym space, to be propagated to the subject's cortical mask. Use this option if the label set contains only cortical labels.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"mni-cortical-labels-2": {
"base": "file",
"description": " One or more cortical label images in the MNI152NLin2009cAsym space, to be propagated to the subject's cortical mask. Use this option if the label set contains only cortical labels.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
},
"mni-cortical-labels-3": {
"base": "file",
"description": " One or more cortical label images in the MNI152NLin2009cAsym space, to be propagated to the subject's cortical mask. Use this option if the label set contains only cortical labels.",
"optional": true,
"type": {
"enum": [
"nifti"
]
}
}
},
"config": {
"template": {
"default": "TxAging",
"description": "NON FUNCTIONAL RIGHT NOW - The template to use for brain extraction and registration.",
"enum": [
"TxAging",
"OASIS30ANTS",
"MNI152NLin2009cAsym",
"NKI"
],
"type": "string"
},
"denoise": {
"default": true,
"description": "Run denoising within the ACT pipeline.",
"type": "boolean"
},
"num-threads": {
"default": 1,
"description": "Maximum number of CPU threads to use. Set to 0 to use as many threads as there are cores",
"type": "integer"
},
"run-quick": {
"default": false,
"description": "'true' to use quick registration, 'false' to use the default registration.",
"type": "boolean"
},
"trim-neck": {
"default": true,
"description": "'true' to run the trim_neck.sh script, 'false' to use the raw data.",
"type": "boolean"
},
"BIDS-subject": {
"default": "",
"description": "The sub- field of the input image filename. Leave blank if the correct file is distinguishable without a sub- field.",
"type": "string"
},
"BIDS-session": {
"default": "",
"description": "The ses- field of the input image filename. Leave blank if the correct file is distinguishable without a ses- field.",
"type": "string"
},
"BIDS-acq": {
"default": "",
"description": "The acq- field of the input image filename. Leave blank if the correct file is distinguishable without an acq- field.",
"type": "string"
},
"BIDS-run": {
"default": "",
"description": "The run- field of the input image filename. Leave blank if there is only one run.",
"type": "string"
}
},
"author": "Tustison, et al. | Modified for Flywheel by Philip Cook, Will Tackett",
"maintainer": "Philip Cook, Will Tackett",
"cite": "Tustison NJ, Cook PA, Klein A, Song G, Das SR, Duda JT, Kandel BM, van Strien N, Stone JR, Gee JC, Avants BB. Large-scale evaluation of ANTs and FreeSurfer cortical thickness measurements. Neuroimage. 2014 Oct 1;99:166-79. doi: 10.1016/j.neuroimage.2014.05.044. Epub 2014 May 29. PMID: 24879923.",
"license": "Apache-2.0",
"source": "https://github.com/willtack/antsct_fw",
"url": "https://doi.org/10.1117/12.2007128",
"custom": {
"gear-builder": {
"category": "analysis",
"image": "willtack/antsct-fw:0.4.0_0.2.0"
},
"flywheel":{"suite": "BrainScienceCenter"}
}
}