fsl-topup/manifest.json at master · flywheel-apps/fsl-topup · GitHub

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{
  "name": "fsl-topup",
  "label": "FSL: TOPUP correction for susceptibility induced distortions",
  "description": "Estimates a distortion correction field given one or more pairs of images with opposite PE directions",
  "author": "FSL",
  "maintainer": "Flywheel <support@flywheel.io>",
  "license": "MIT",
  "source": "https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/topup",
  "url": "https://github.com/flywheel-apps/fsl-topup",
  "version": "0.0.6",
  "environment": {},
  "custom": {
    "gear-builder": {
      "category": "analysis",
      "image": "flywheel/fsl-topup:0.0.6_5.0.10"
    },
    "docker-image": "flywheel/fsl-topup:0.0.6_5.0.10",
    "flywheel": {
      "suite": "Image Processing",
      "classification": {
        "species": [
          "Human",
          "Animal"
        ],
        "organ": [
          "Brain"
        ],
        "therapeutic_area": [
          "Neurology",
          "Psychiatry/Psychology"
        ],
        "modality": [
          "MR"
        ],
        "function": [
          "Image Processing - Functional",
          "Image Processing - Diffusion",
          "Image Processing - Structural"
        ]
      }
    }
  },
  "inputs": {
    "image_1": {
      "base": "file",
      "description": "first image in an pair of images with opposite phase encoding direction",
      "optional": false,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "image_2": {
      "base": "file",
      "description": "second image in an pair of images with opposite phase encoding direction",
      "optional": false,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "apply_to_1": {
      "base": "file",
      "description": "an image to apply the TOPUP correction to using this fieldmap.  Should have the same PE direction as image 1",
      "optional": true,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "apply_to_2": {
      "base": "file",
      "description": "an image to apply the TOPUP correction to using this fieldmap.  Should have the same PE direction as image 2",
      "optional": true,
      "type": {
        "enum": [
          "nifti"
        ]
      }
    },
    "config_file": {
      "base": "file",
      "description": "A configuration file is a text file containing some or all of the parameters that can be specified for topup. The name of the file should be passed as argument to the --config parameter. It should be an ascii-file with one row for each parameter, and where comments (ignored by topup) are preceeded by a #.",
      "optional": true,
      "type": {
        "enum": [
          "text",
          ""
        ]
      }
    },
    "acquisition_parameters": {
      "base": "file",
      "description": "This parameter specifies a text-file that contains information about how the volumes were acquired.  Row 1 is for image 1, row 2 is for image 2",
      "optional": true,
      "type": {
        "enum": [
          "text",
          ""
        ]
      }
    }
  },
  "config": {
    "gear-log-level": {
      "default": "INFO",
      "description": "Gear Log verbosity level (ERROR|WARNING|INFO|DEBUG)",
      "type": "string",
      "enum": [
        "ERROR",
        "WARNING",
        "INFO",
        "DEBUG"
      ]
    },
    "topup_only": {
      "default": false,
      "description": "only run topup and get fieldmaps (do no correct images)",
      "type": "boolean"
    },
    "displacement_field": {
      "default": false,
      "description": "save displacement fields",
      "type": "boolean"
    },
    "jacobian_determinants": {
      "default": false,
      "description": "save jacobian determinants",
      "type": "boolean"
    },
    "rigid_body_matrix": {
      "default": true,
      "description": "save rigid body transformation matricies to align volumes",
      "type": "boolean"
    },
    "verbose": {
      "default": false,
      "description": "output verbose information to the log",
      "type": "boolean"
    },
    "topup_debug_level": {
      "default": 0,
      "description": "Topup Log verbosity level (0|1|2|3)",
      "type": "integer",
      "enum": [
        0,
        1,
        2,
        3
      ]
    },
    "QA": {
      "default": true,
      "description": "Save a topup QA image comparing distorted to corrected images",
      "type": "boolean"
    }
  },
  "command": "source /venv/bin/activate && python run.py"
}