.. AUTO-GENERATED FILE -- DO NOT EDIT!

interfaces.niftyfit.qt1
=======================


.. _nipype.interfaces.niftyfit.qt1.FitQt1:


.. index:: FitQt1

FitQt1
------

`Link to code <file:///build/nipype-1.1.8/nipype/interfaces/niftyfit/qt1.py#L161>`__

Wraps the executable 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 <https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release>`_

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.
                argument: ``-source %s``, position: 1

        [Optional]
        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.
                argument: ``-voxel %d %d %d``, position: 10
        comp_file: (a file name)
                Filename of the estimated multi-component T1 map.
                argument: ``-comp %s``
        mcout: (a file name)
                Filename of mc samples (ascii text file)
                argument: ``-mcout %s``
        t1_list: (a file name)
                Filename of list of pre-defined T1s
                argument: ``-T1list %s``
        gn_flag: (a boolean)
                Use Gauss-Newton algorithm [Levenberg-Marquardt].
                argument: ``-gn``, position: 8
        flips: (a list of items which are a float)
                Flip angles
                argument: ``-flips %s``
        m0map_file: (a file name)
                Filename of the estimated input M0 map.
                argument: ``-m0map %s``
        maxit: (an integer (int or long))
                NLSQR iterations [100].
                argument: ``-maxit %d``, position: 11
        te_value: (a float)
                TE Echo Time [0ms!].
                argument: ``-TE %f``, position: 4
        t1map_file: (a file name)
                Filename of the estimated output T1 map (in ms).
                argument: ``-t1map %s``
        flips_list: (a file name)
                Filename of list of pre-defined flip angles (deg).
                argument: ``-fliplist %s``
        spgr: (a boolean)
                Spoiled Gradient Echo fitting
                argument: ``-SPGR``
        mcmap_file: (a file name)
                Filename of the estimated output multi-parameter map.
                argument: ``-mcmap %s``
        acceptance: (a float)
                Fraction of iterations to accept [0.23].
                argument: ``-acceptance %f``
        mcsamples: (an integer (int or long))
                Number of samples to keep [100].
                argument: ``-mcsamples %d``
        t1min: (a float)
                Minimum tissue T1 value [400ms].
                argument: ``-T1min %f``
        tis: (a list of items which are a float)
                Inversion times for T1 data [1s,2s,5s].
                argument: ``-TIs %s``, position: 14
        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
        b1map: (a file name)
                Filename of B1 estimate for fitting (or include in prior).
                argument: ``-b1map %s``
        t1max: (a float)
                Maximum tissue T1 value [4000ms].
                argument: ``-T1max %f``
        tis_list: (a file name)
                Filename of list of pre-defined TIs.
                argument: ``-TIlist %s``
        nb_comp: (an integer (int or long))
                Number of components to fit [1] (currently IR/SR only)
                argument: ``-nc %d``, position: 6
        args: (a unicode string)
                Additional parameters to the command
                argument: ``%s``
        error_file: (a file name)
                Filename of the error map (symmetric matrix, [Diag,OffDiag]).
                argument: ``-error %s``
        syn_file: (a file name)
                Filename of the synthetic ASL data.
                argument: ``-syn %s``
        sr_flag: (a boolean)
                Saturation Recovery fitting [default].
                argument: ``-SR``, position: 12
        slice_no: (an integer (int or long))
                Fit to single slice number.
                argument: ``-slice %d``, position: 9
        ir_flag: (a boolean)
                Inversion Recovery fitting [default].
                argument: ``-IR``, position: 13
        lm_val: (a tuple of the form: (a float, a float))
                Set LM parameters (initial value, decrease rate) [100,1.2].
                argument: ``-lm %f %f``, position: 7
        mcmaxit: (an integer (int or long))
                Number of iterations to run [10,000].
                argument: ``-mcmaxit %d``
        mask: (an existing file name)
                Filename of image mask.
                argument: ``-mask %s``, position: 2
        prior: (an existing file name)
                Filename of parameter prior.
                argument: ``-prior %s``, position: 3
        tr_value: (a float)
                TR Repetition Time [10s!].
                argument: ``-TR %f``, position: 5
        res_file: (a file name)
                Filename of the model fit residuals
                argument: ``-res %s``

Outputs::

        t1map_file: (a file name)
                Filename of the estimated output T1 map (in ms)
        comp_file: (a file name)
                Filename of the estimated multi-component T1 map.
        mcmap_file: (a file name)
                Filename of the estimated output multi-parameter 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
        syn_file: (a file name)
                Filename of the synthetic ASL data
        res_file: (a file name)
                Filename of the model fit residuals
