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# interfaces.niftyfit.qt1

## FitQt1

Link to code

Wraps command fit_qt1

Interface for executable fit_qt1 from Niftyfit platform.

Use NiftyFit to perform Qt1 fitting.

T1 Fitting Routine (To inversion recovery or spgr data). Fits single component T1 maps in the first instance.

Source code

### Examples

    >>> from nipype.interfaces.niftyfit import FitQt1
    >>> fit_qt1 = FitQt1()
    >>> fit_qt1.inputs.source_file = 'TI4D.nii.gz'
    >>> fit_qt1.cmdline
    'fit_qt1 -source TI4D.nii.gz -comp TI4D_comp.nii.gz -error TI4D_error.nii.gz -m0map TI4D_m0map.nii.gz -mcmap TI4D_mcmap.nii.gz -res TI4D_res.nii.gz -syn TI4D_syn.nii.gz -t1map TI4D_t1map.nii.gz'

Inputs:

    [Mandatory]
    source_file: (an existing file name)
            Filename of the 4D Multi-Echo T1 source image.
            flag: -source %s, position: 1

    [Optional]
    acceptance: (a float)
            Fraction of iterations to accept [0.23].
            flag: -acceptance %f
    args: (a unicode string)
            Additional parameters to the command
            flag: %s
    b1map: (a file name)
            Filename of B1 estimate for fitting (or include in prior).
            flag: -b1map %s
    comp_file: (a file name)
            Filename of the estimated multi-component T1 map.
            flag: -comp %s
    environ: (a dictionary with keys which are a newbytes or None or a
             newstr or None and with values which are a newbytes or None or a
             newstr or None, nipype default value: {})
            Environment variables
    error_file: (a file name)
            Filename of the error map (symmetric matrix, [Diag,OffDiag]).
            flag: -error %s
    flips: (a list of items which are a float)
            Flip angles
            flag: -flips %s
    flips_list: (a file name)
            Filename of list of pre-defined flip angles (deg).
            flag: -fliplist %s
    gn_flag: (a boolean)
            Use Gauss-Newton algorithm [Levenberg-Marquardt].
            flag: -gn, position: 8
    ignore_exception: (a boolean, nipype default value: False)
            Print an error message instead of throwing an exception in case the
            interface fails to run
    ir_flag: (a boolean)
            Inversion Recovery fitting [default].
            flag: -IR, position: 13
    lm_val: (a tuple of the form: (a float, a float))
            Set LM parameters (initial value, decrease rate) [100,1.2].
            flag: -lm %f %f, position: 7
    m0map_file: (a file name)
            Filename of the estimated input M0 map.
            flag: -m0map %s
    mask: (an existing file name)
            Filename of image mask.
            flag: -mask %s, position: 2
    maxit: (an integer (int or long))
            NLSQR iterations [100].
            flag: -maxit %d, position: 11
    mcmap_file: (a file name)
            Filename of the estimated output multi-parameter map.
            flag: -mcmap %s
    mcmaxit: (an integer (int or long))
            Number of iterations to run [10,000].
            flag: -mcmaxit %d
    mcout: (a file name)
            Filename of mc samples (ascii text file)
            flag: -mcout %s
    mcsamples: (an integer (int or long))
            Number of samples to keep [100].
            flag: -mcsamples %d
    nb_comp: (an integer (int or long))
            Number of components to fit [1] (currently IR/SR only)
            flag: -nc %d, position: 6
    prior: (an existing file name)
            Filename of parameter prior.
            flag: -prior %s, position: 3
    res_file: (a file name)
            Filename of the model fit residuals
            flag: -res %s
    slice_no: (an integer (int or long))
            Fit to single slice number.
            flag: -slice %d, position: 9
    spgr: (a boolean)
            Spoiled Gradient Echo fitting
            flag: -SPGR
    sr_flag: (a boolean)
            Saturation Recovery fitting [default].
            flag: -SR, position: 12
    syn_file: (a file name)
            Filename of the synthetic ASL data.
            flag: -syn %s
    t1_list: (a file name)
            Filename of list of pre-defined T1s
            flag: -T1list %s
    t1map_file: (a file name)
            Filename of the estimated output T1 map (in ms).
            flag: -t1map %s
    t1max: (a float)
            Maximum tissue T1 value [4000ms].
            flag: -T1max %f
    t1min: (a float)
            Minimum tissue T1 value [400ms].
            flag: -T1min %f
    te_value: (a float)
            TE Echo Time [0ms!].
            flag: -TE %f, position: 4
    terminal_output: (u'stream' or u'allatonce' or u'file' or u'none')
            Control terminal output: `stream` - displays to terminal immediately
            (default), `allatonce` - waits till command is finished to display
            output, `file` - writes output to file, `none` - output is ignored
    tis: (a list of items which are a float)
            Inversion times for T1 data [1s,2s,5s].
            flag: -TIs %s, position: 14
    tis_list: (a file name)
            Filename of list of pre-defined TIs.
            flag: -TIlist %s
    tr_value: (a float)
            TR Repetition Time [10s!].
            flag: -TR %f, position: 5
    voxel: (a tuple of the form: (an integer (int or long), an integer
             (int or long), an integer (int or long)))
            Fit to single voxel only.
            flag: -voxel %d %d %d, position: 10

Outputs:

    comp_file: (a file name)
            Filename of the estimated multi-component T1 map.
    error_file: (a file name)
            Filename of the error map (symmetric matrix, [Diag,OffDiag])
    m0map_file: (a file name)
            Filename of the m0 map
    mcmap_file: (a file name)
            Filename of the estimated output multi-parameter map
    res_file: (a file name)
            Filename of the model fit residuals
    syn_file: (a file name)
            Filename of the synthetic ASL data
    t1map_file: (a file name)
            Filename of the estimated output T1 map (in ms)