manifest.json

{
  "author": "Analysis Group, FMRIB, Oxford, UK.",
  "config": {
    "BB_THRESH": {
      "default": 10,
      "description": "SET THE BRAIN BACKGROUND THRESHOLD. This is used in intensity normalisation, brain mask generation and various other places in the analysis. [Default=10]",
      "type": "number"
    },
    "BET": {
      "default": 1,
      "description": "RUN BRAIN EXTRACTION USING FSL's BET [1=yes, 0=no. default=1]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "DOF": {
      "default": 12,
      "description": "Degrees of Freedom for registration to standard space (allowed: 3, 6, 12)",
      "type": "integer",
      "enum": [
        3,
        6,
        12
      ]
    },
    "FNIRT": {
      "default": 0,
      "description": "Do nonlinear registration from structural to standard space? (default no = 0)",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "FWHM": {
      "default": 5,
      "description": "FWHM FOR SPATIAL SMOOTHING (mm) [default=5]",
      "type": "number"
    },
    "HPF": {
      "default": 1,
      "description": "RUN HIGHPASS FILTERING [1=yes, 0=no. default=1]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "HPF_CUTOFF": {
      "default": 100,
      "description": "HIGHPASS FILTER CUTOFF (seconds) [default=100]",
      "type": "number"
    },
    "INT_NORM": {
      "default": 1,
      "description": "RUN INTENSITY NORMALIZATION [1=yes, 0=no. default=1]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "LPF": {
      "default": 0,
      "description": "RUN LOWPASS FILTERING [1=yes, 0=no. default=0]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "MC": {
      "default": 1,
      "description": "RUN MOTION CORRECTION [1=yes, 0=no. default=1]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "NOISE_LVL": {
      "default": 0.66,
      "description": "SET THE FMRI NOISE LEVEL. The standard deviation (over time) for a typical voxel, expressed as a percentage of the baseline signal level. [default=0.66]",
      "type": "number"
    },
    "REG_STANDARD_IMAGE": {
      "default": 1,
      "description": "REGISTER TO A STANDARD IMAGE [1=yes, 0=no. default=1]. If Standard Template not supplied as an input, MNI152 2mm will be used.",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "SEARCH_SPACE": {
      "default": 90,
      "description": "Search space for registration to initial structural. 0 = no search; 90 = normal search; 180 = full search",
      "type": "integer",
      "enum": [
        0,
        90,
        180
      ]
    },
    "STC": {
      "default": 1,
      "description": "RUN SLICE TIMING CORRECTION 0 = None. 1 = Regular up (0, 1, 2, 3, ...). 2 = Regular down. 3 = Use slice order file. 4 = Use slice timings file. 5 = Interleaved (0, 2, 4 ... 1, 3, 5 ... )",
      "type": "integer"
    },
    "T_SMOOTH": {
      "default": 0.34,
      "description": "SET TNE TEMPORAL SMOOTHNESS is the smoothness coefficient in a simple AR(1) autocorrelation model (much simpler than that actually used in the FILM timeseries analysis but good enough for the efficiency calculation here). [default=0.34]",
      "type": "number"
    },
    "Use_alt_template": {
      "default": 0,
      "description": "Use the specified template (from the inputs tab) to register the images. [1=yes, 0=no. default=0]",
      "maximum": 1,
      "minimum": 0,
      "type": "integer"
    },
    "Z_THRESH": {
      "default": 5.3,
      "description": "SET THE Z THRESHOLD FOR DESIGN EFFICIENCY CALCULATION. Used to determine what level of activation would be statistically significant, to be used only in the design efficiency calculation. Increasing this will result in higher estimates of required effect. [default=5.3]",
      "type": "number"
    }
  },
  "custom": {
    "flywheel": {
      "classification": {
        "species": [
          "Animal",
          "Human"
        ],
        "organ": [
          "Brain"
        ],
        "therapeutic_area": [
          "Psychiatry/Psychology",
          "Neurology"
        ],
        "modality": [
          "MR"
        ],
        "function": [
          "Image Processing - Functional"
        ]
      },
      "components": [
        "FSL"
      ],
      "modality": [
        "MR"
      ],
      "suite": "Image Processing",
      "type": [
        "NIFTI"
      ]
    },
    "gear-builder": {
      "category": "analysis",
      "image": "flywheel/fsl-feat:1.0.4_6.0"
    }
  },
  "description": "FSL's FEAT (FMRI Expert Analysis Tool). As implemented in this Gear FEAT allows for basic preprocessing of an fMRI dataset including motion correction using MCFLIRT [Jenkinson 2002]; slice-timing correction using Fourier-space time-series phase-shifting; non-brain removal using BET [Smith 2002]; spatial smoothing using a Gaussian kernel; multiplicative mean intensity normalization of the volume at each timepoint; and highpass temporal filtering (Gaussian-weighted least-squares straight line fitting), brain extraction, and registration to a standard image (MNI152). LICENSING NOTE: FSL software are owned by Oxford University Innovation and license is required for any commercial applications. For commercial licence please contact fsl@innovation.ox.ac.uk. For academic use, an academic license is required which is available by registering on the FSL website. Any use of the software requires that the user obtain the appropriate license. See https://fsl.fmrib.ox.ac.uk/fsldownloads_registration for more information.",
  "inputs": {
    "NIFTI": {
      "base": "file",
      "description": "FUNCTIONAL NIfTI file to be processed.",
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "SLICE_FILE": {
      "base": "file",
      "description": "SLICE ORDER/TIMING FILE. Must set STC config option to 3.",
      "optional": true,
      "type": {
        "enum": [
          "text"
        ]
      }
    },
    "STANDARD_TEMPLATE": {
      "base": "file",
      "description": "Template to which other images are registered. Must set REG_STANDARD_IMAGE to 1.",
      "optional": true,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    }
  },
  "label": "FSL: FEAT - fMRI preprocessing (v6.0)",
  "license": "Apache-2.0",
  "maintainer": "Flywheel <support@flywheel.io>",
  "name": "fsl-feat",
  "source": "http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FEAT",
  "url": "https://github.com/flywheel-apps/fsl-feat",
  "version": "1.0.4_6.0"
}