{
    "name": "FLIRT",
    "command-line": "flirt [ANGLE_REP] [APPLY_ISOXFM] [APPLY_XFM] [BBRSLOPE] [BBRTYPE] [BGVALUE] [BINS] [COARSE_SEARCH] [COST] [COST_FUNC] [DATATYPE] [DOF] [ECHOSPACING] [FIELDMAP] [FIELDMAPMASK] [FINE_SEARCH] [FORCE_SCALING] [IN_FILE] [IN_MATRIX_FILE] [IN_WEIGHT] [INTERP] [MIN_SAMPLING] [NO_CLAMP] [NO_RESAMPLE] [NO_RESAMPLE_BLUR] [NO_SEARCH] [PADDING_SIZE] [PEDIR] [REF_WEIGHT] [REFERENCE] [RIGID2D] [SCHEDULE] [SEARCHR_X] [SEARCHR_Y] [SEARCHR_Z] [SINC_WIDTH] [SINC_WINDOW] [USES_QFORM] [VERBOSE] [WM_SEG] [WMCOORDS] [WMNORMS] [OUT_FILE] [OUT_MATRIX_FILE]",
    "author": "Nipype (interface), Oxford Centre for Functional MRI of the Brain (FMRIB) (tool)",
    "description": "FLIRT, as implemented in Nipype (module: nipype.interfaces.fsl, interface: FLIRT).",
    "inputs": [
        {
            "id": "angle_rep",
            "name": "Angle rep",
            "type": "String",
            "value-key": "[ANGLE_REP]",
            "command-line-flag": "-anglerep",
            "description": "'quaternion' or 'euler'. Representation of rotation angles.",
            "optional": true,
            "value-choices": [
                "quaternion",
                "euler"
            ]
        },
        {
            "id": "apply_isoxfm",
            "name": "Apply isoxfm",
            "type": "Number",
            "value-key": "[APPLY_ISOXFM]",
            "command-line-flag": "-applyisoxfm",
            "description": "A float. As applyxfm but forces isotropic resampling.",
            "optional": true
        },
        {
            "id": "apply_xfm",
            "name": "Apply xfm",
            "type": "Flag",
            "value-key": "[APPLY_XFM]",
            "command-line-flag": "-applyxfm",
            "description": "A boolean. Apply transformation supplied by in_matrix_file or uses_qform to use the affine matrix stored in the reference header.",
            "optional": true
        },
        {
            "id": "bbrslope",
            "name": "Bbrslope",
            "type": "Number",
            "value-key": "[BBRSLOPE]",
            "command-line-flag": "-bbrslope",
            "description": "A float. Value of bbr slope.",
            "optional": true
        },
        {
            "id": "bbrtype",
            "name": "Bbrtype",
            "type": "String",
            "value-key": "[BBRTYPE]",
            "command-line-flag": "-bbrtype",
            "description": "'signed' or 'global_abs' or 'local_abs'. Type of bbr cost function: signed [default], global_abs, local_abs.",
            "optional": true,
            "value-choices": [
                "signed",
                "global_abs",
                "local_abs"
            ]
        },
        {
            "id": "bgvalue",
            "name": "Bgvalue",
            "type": "Number",
            "value-key": "[BGVALUE]",
            "command-line-flag": "-setbackground",
            "description": "A float. Use specified background value for points outside fov.",
            "optional": true
        },
        {
            "id": "bins",
            "name": "Bins",
            "type": "Number",
            "integer": true,
            "value-key": "[BINS]",
            "command-line-flag": "-bins",
            "description": "An integer (int or long). Number of histogram bins.",
            "optional": true
        },
        {
            "id": "coarse_search",
            "name": "Coarse search",
            "type": "Number",
            "integer": true,
            "value-key": "[COARSE_SEARCH]",
            "command-line-flag": "-coarsesearch",
            "description": "An integer (int or long). Coarse search delta angle.",
            "optional": true
        },
        {
            "id": "cost",
            "name": "Cost",
            "type": "String",
            "value-key": "[COST]",
            "command-line-flag": "-cost",
            "description": "'mutualinfo' or 'corratio' or 'normcorr' or 'normmi' or 'leastsq' or 'labeldiff' or 'bbr'. Cost function.",
            "optional": true,
            "value-choices": [
                "mutualinfo",
                "corratio",
                "normcorr",
                "normmi",
                "leastsq",
                "labeldiff",
                "bbr"
            ]
        },
        {
            "id": "cost_func",
            "name": "Cost func",
            "type": "String",
            "value-key": "[COST_FUNC]",
            "command-line-flag": "-searchcost",
            "description": "'mutualinfo' or 'corratio' or 'normcorr' or 'normmi' or 'leastsq' or 'labeldiff' or 'bbr'. Cost function.",
            "optional": true,
            "value-choices": [
                "mutualinfo",
                "corratio",
                "normcorr",
                "normmi",
                "leastsq",
                "labeldiff",
                "bbr"
            ]
        },
        {
            "id": "datatype",
            "name": "Datatype",
            "type": "String",
            "value-key": "[DATATYPE]",
            "command-line-flag": "-datatype",
            "description": "'char' or 'short' or 'int' or 'float' or 'double'. Force output data type.",
            "optional": true,
            "value-choices": [
                "char",
                "short",
                "int",
                "float",
                "double"
            ]
        },
        {
            "id": "dof",
            "name": "Dof",
            "type": "Number",
            "integer": true,
            "value-key": "[DOF]",
            "command-line-flag": "-dof",
            "description": "An integer (int or long). Number of transform degrees of freedom.",
            "optional": true
        },
        {
            "id": "echospacing",
            "name": "Echospacing",
            "type": "Number",
            "value-key": "[ECHOSPACING]",
            "command-line-flag": "-echospacing",
            "description": "A float. Value of epi echo spacing - units of seconds.",
            "optional": true
        },
        {
            "id": "fieldmap",
            "name": "Fieldmap",
            "type": "File",
            "value-key": "[FIELDMAP]",
            "command-line-flag": "-fieldmap",
            "description": "A file name. Fieldmap image in rads/s - must be already registered to the reference image.",
            "optional": true
        },
        {
            "id": "fieldmapmask",
            "name": "Fieldmapmask",
            "type": "File",
            "value-key": "[FIELDMAPMASK]",
            "command-line-flag": "-fieldmapmask",
            "description": "A file name. Mask for fieldmap image.",
            "optional": true
        },
        {
            "id": "fine_search",
            "name": "Fine search",
            "type": "Number",
            "integer": true,
            "value-key": "[FINE_SEARCH]",
            "command-line-flag": "-finesearch",
            "description": "An integer (int or long). Fine search delta angle.",
            "optional": true
        },
        {
            "id": "force_scaling",
            "name": "Force scaling",
            "type": "Flag",
            "value-key": "[FORCE_SCALING]",
            "command-line-flag": "-forcescaling",
            "description": "A boolean. Force rescaling even for low-res images.",
            "optional": true
        },
        {
            "id": "in_file",
            "name": "In file",
            "type": "File",
            "value-key": "[IN_FILE]",
            "command-line-flag": "-in",
            "description": "An existing file name. Input file.",
            "optional": false
        },
        {
            "id": "in_matrix_file",
            "name": "In matrix file",
            "type": "File",
            "value-key": "[IN_MATRIX_FILE]",
            "command-line-flag": "-init",
            "description": "A file name. Input 4x4 affine matrix.",
            "optional": true
        },
        {
            "id": "in_weight",
            "name": "In weight",
            "type": "File",
            "value-key": "[IN_WEIGHT]",
            "command-line-flag": "-inweight",
            "description": "An existing file name. File for input weighting volume.",
            "optional": true
        },
        {
            "id": "interp",
            "name": "Interp",
            "type": "String",
            "value-key": "[INTERP]",
            "command-line-flag": "-interp",
            "description": "'trilinear' or 'nearestneighbour' or 'sinc' or 'spline'. Final interpolation method used in reslicing.",
            "optional": true,
            "value-choices": [
                "trilinear",
                "nearestneighbour",
                "sinc",
                "spline"
            ]
        },
        {
            "id": "min_sampling",
            "name": "Min sampling",
            "type": "Number",
            "value-key": "[MIN_SAMPLING]",
            "command-line-flag": "-minsampling",
            "description": "A float. Set minimum voxel dimension for sampling.",
            "optional": true
        },
        {
            "id": "no_clamp",
            "name": "No clamp",
            "type": "Flag",
            "value-key": "[NO_CLAMP]",
            "command-line-flag": "-noclamp",
            "description": "A boolean. Do not use intensity clamping.",
            "optional": true
        },
        {
            "id": "no_resample",
            "name": "No resample",
            "type": "Flag",
            "value-key": "[NO_RESAMPLE]",
            "command-line-flag": "-noresample",
            "description": "A boolean. Do not change input sampling.",
            "optional": true
        },
        {
            "id": "no_resample_blur",
            "name": "No resample blur",
            "type": "Flag",
            "value-key": "[NO_RESAMPLE_BLUR]",
            "command-line-flag": "-noresampblur",
            "description": "A boolean. Do not use blurring on downsampling.",
            "optional": true
        },
        {
            "id": "no_search",
            "name": "No search",
            "type": "Flag",
            "value-key": "[NO_SEARCH]",
            "command-line-flag": "-nosearch",
            "description": "A boolean. Set all angular searches to ranges 0 to 0.",
            "optional": true
        },
        {
            "id": "padding_size",
            "name": "Padding size",
            "type": "Number",
            "integer": true,
            "value-key": "[PADDING_SIZE]",
            "command-line-flag": "-paddingsize",
            "description": "An integer (int or long). For applyxfm: interpolates outside image by size.",
            "optional": true
        },
        {
            "id": "pedir",
            "name": "Pedir",
            "type": "Number",
            "integer": true,
            "value-key": "[PEDIR]",
            "command-line-flag": "-pedir",
            "description": "An integer (int or long). Phase encode direction of epi - 1/2/3=x/y/z & -1/-2/-3=-x/-y/-z.",
            "optional": true
        },
        {
            "id": "ref_weight",
            "name": "Ref weight",
            "type": "File",
            "value-key": "[REF_WEIGHT]",
            "command-line-flag": "-refweight",
            "description": "An existing file name. File for reference weighting volume.",
            "optional": true
        },
        {
            "id": "reference",
            "name": "Reference",
            "type": "File",
            "value-key": "[REFERENCE]",
            "command-line-flag": "-ref",
            "description": "An existing file name. Reference file.",
            "optional": false
        },
        {
            "id": "rigid2D",
            "name": "Rigid2d",
            "type": "Flag",
            "value-key": "[RIGID2D]",
            "command-line-flag": "-2D",
            "description": "A boolean. Use 2d rigid body mode - ignores dof.",
            "optional": true
        },
        {
            "id": "schedule",
            "name": "Schedule",
            "type": "File",
            "value-key": "[SCHEDULE]",
            "command-line-flag": "-schedule",
            "description": "An existing file name. Replaces default schedule.",
            "optional": true
        },
        {
            "id": "searchr_x",
            "name": "Searchr x",
            "type": "Number",
            "list": true,
            "integer": true,
            "min-list-entries": 2,
            "max-list-entries": 2,
            "value-key": "[SEARCHR_X]",
            "command-line-flag": "-searchrx",
            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along x-axis, in degrees.",
            "optional": true
        },
        {
            "id": "searchr_y",
            "name": "Searchr y",
            "type": "Number",
            "list": true,
            "integer": true,
            "min-list-entries": 2,
            "max-list-entries": 2,
            "value-key": "[SEARCHR_Y]",
            "command-line-flag": "-searchry",
            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along y-axis, in degrees.",
            "optional": true
        },
        {
            "id": "searchr_z",
            "name": "Searchr z",
            "type": "Number",
            "list": true,
            "integer": true,
            "min-list-entries": 2,
            "max-list-entries": 2,
            "value-key": "[SEARCHR_Z]",
            "command-line-flag": "-searchrz",
            "description": "A list of from 2 to 2 items which are an integer (int or long). Search angles along z-axis, in degrees.",
            "optional": true
        },
        {
            "id": "sinc_width",
            "name": "Sinc width",
            "type": "Number",
            "integer": true,
            "value-key": "[SINC_WIDTH]",
            "command-line-flag": "-sincwidth",
            "description": "An integer (int or long). Full-width in voxels.",
            "optional": true
        },
        {
            "id": "sinc_window",
            "name": "Sinc window",
            "type": "String",
            "value-key": "[SINC_WINDOW]",
            "command-line-flag": "-sincwindow",
            "description": "'rectangular' or 'hanning' or 'blackman'. Sinc window.",
            "optional": true,
            "value-choices": [
                "rectangular",
                "hanning",
                "blackman"
            ]
        },
        {
            "id": "uses_qform",
            "name": "Uses qform",
            "type": "Flag",
            "value-key": "[USES_QFORM]",
            "command-line-flag": "-usesqform",
            "description": "A boolean. Initialize using sform or qform.",
            "optional": true
        },
        {
            "id": "verbose",
            "name": "Verbose",
            "type": "Number",
            "integer": true,
            "value-key": "[VERBOSE]",
            "command-line-flag": "-verbose",
            "description": "An integer (int or long). Verbose mode, 0 is least.",
            "optional": true
        },
        {
            "id": "wm_seg",
            "name": "Wm seg",
            "type": "File",
            "value-key": "[WM_SEG]",
            "command-line-flag": "-wmseg",
            "description": "A file name. White matter segmentation volume needed by bbr cost function.",
            "optional": true
        },
        {
            "id": "wmcoords",
            "name": "Wmcoords",
            "type": "File",
            "value-key": "[WMCOORDS]",
            "command-line-flag": "-wmcoords",
            "description": "A file name. White matter boundary coordinates for bbr cost function.",
            "optional": true
        },
        {
            "id": "wmnorms",
            "name": "Wmnorms",
            "type": "File",
            "value-key": "[WMNORMS]",
            "command-line-flag": "-wmnorms",
            "description": "A file name. White matter boundary normals for bbr cost function.",
            "optional": true
        }
    ],
    "output-files": [
        {
            "name": "Out file",
            "id": "out_file",
            "path-template": "[IN_FILE]_flirt",
            "path-template-stripped-extensions": [
                ".nii.gz",
                ".nii"
            ],
            "optional": true,
            "description": "An existing file name. Path/name of registered file (if generated).",
            "value-key": "[OUT_FILE]",
            "command-line-flag": "-out"
        },
        {
            "name": "Out matrix file",
            "id": "out_matrix_file",
            "path-template": "[IN_FILE]_flirt.mat",
            "path-template-stripped-extensions": [
                ".nii.gz",
                ".nii"
            ],
            "optional": true,
            "description": "An existing file name. Path/name of calculated affine transform (if generated).",
            "value-key": "[OUT_MATRIX_FILE]",
            "command-line-flag": "-omat"
        }
    ],
    "groups": [
        {
            "id": "mutex_group",
            "name": "Mutex group",
            "members": [
                "apply_xfm",
                "apply_isoxfm"
            ],
            "mutually-exclusive": true
        }
    ],
    "tool-version": "1.0.0",
    "schema-version": "0.5",
    "container-image": {
        "image": "mcin/docker-fsl:latest",
        "type": "docker",
        "index": "index.docker.io"
    },
    "tags": {
        "domain": [
            "neuroinformatics",
            "fmri"
        ],
        "source": "nipype-interface"
    }
}