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# nipype.interfaces.niftyfit.qt1 module

The QT1 module of niftyfit, which wraps the Multi-Echo T1 fitting methods in NiftyFit.

## FitQt1

Link to code

> Bases: NiftyFitCommand

> Wrapped executable: `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'

> source_filea pathlike object or string representing an existing file

>   Filename of the 4D Multi-Echo T1 source image. Maps to a command-line argument: `-source %s` (position: 1).

> acceptancea float

>   Fraction of iterations to accept [0.23]. Maps to a command-line argument: `-acceptance %f`.

> argsa string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> b1mapa pathlike object or string representing an existing file

>   Filename of B1 estimate for fitting (or include in prior). Maps to a command-line argument: `-b1map %s`.

> comp_filea pathlike object or string representing a file

>   Filename of the estimated multi-component T1 map. Maps to a command-line argument: `-comp %s`.

> environa dictionary with keys which are a bytes or None or a value of class ‘str’ and with values which are a bytes or None or a value of class ‘str’

>   Environment variables. (Nipype default value: `{}`)

> error_filea pathlike object or string representing a file

>   Filename of the error map (symmetric matrix, [Diag,OffDiag]). Maps to a command-line argument: `-error %s`.

> flipsa list of items which are a float

>   Flip angles. Maps to a command-line argument: `-flips %s`.

> flips_lista pathlike object or string representing an existing file

>   Filename of list of pre-defined flip angles (deg). Maps to a command-line argument: `-fliplist %s`.

> gn_flaga boolean

>   Use Gauss-Newton algorithm [Levenberg-Marquardt]. Maps to a command-line argument: `-gn` (position: 8).

> ir_flaga boolean

>   Inversion Recovery fitting [default]. Maps to a command-line argument: `-IR` (position: 13).

> lm_vala tuple of the form: (a float, a float)

>   Set LM parameters (initial value, decrease rate) [100,1.2]. Maps to a command-line argument: `-lm %f %f` (position: 7).

> m0map_filea pathlike object or string representing a file

>   Filename of the estimated input M0 map. Maps to a command-line argument: `-m0map %s`.

> maska pathlike object or string representing an existing file

>   Filename of image mask. Maps to a command-line argument: `-mask %s` (position: 2).

> maxitan integer

>   NLSQR iterations [100]. Maps to a command-line argument: `-maxit %d` (position: 11).

> mcmap_filea pathlike object or string representing a file

>   Filename of the estimated output multi-parameter map. Maps to a command-line argument: `-mcmap %s`.

> mcmaxitan integer

>   Number of iterations to run [10,000]. Maps to a command-line argument: `-mcmaxit %d`.

> mcouta pathlike object or string representing an existing file

>   Filename of mc samples (ascii text file). Maps to a command-line argument: `-mcout %s`.

> mcsamplesan integer

>   Number of samples to keep [100]. Maps to a command-line argument: `-mcsamples %d`.

> nb_compan integer

>   Number of components to fit [1] (currently IR/SR only). Maps to a command-line argument: `-nc %d` (position: 6).

> priora pathlike object or string representing an existing file

>   Filename of parameter prior. Maps to a command-line argument: `-prior %s` (position: 3).

> res_filea pathlike object or string representing a file

>   Filename of the model fit residuals. Maps to a command-line argument: `-res %s`.

> slice_noan integer

>   Fit to single slice number. Maps to a command-line argument: `-slice %d` (position: 9).

> spgra boolean

>   Spoiled Gradient Echo fitting. Maps to a command-line argument: `-SPGR`.

> sr_flaga boolean

>   Saturation Recovery fitting [default]. Maps to a command-line argument: `-SR` (position: 12).

> syn_filea pathlike object or string representing a file

>   Filename of the synthetic ASL data. Maps to a command-line argument: `-syn %s`.

> t1_lista pathlike object or string representing an existing file

>   Filename of list of pre-defined T1s. Maps to a command-line argument: `-T1list %s`.

> t1map_filea pathlike object or string representing a file

>   Filename of the estimated output T1 map (in ms). Maps to a command-line argument: `-t1map %s`.

> t1maxa float

>   Maximum tissue T1 value [4000ms]. Maps to a command-line argument: `-T1max %f`.

> t1mina float

>   Minimum tissue T1 value [400ms]. Maps to a command-line argument: `-T1min %f`.

> te_valuea float

>   TE Echo Time [0ms!]. Maps to a command-line argument: `-TE %f` (position: 4).

> tisa list of items which are a float

>   Inversion times for T1 data [1s,2s,5s]. Maps to a command-line argument: `-TIs %s` (position: 14).

> tis_lista pathlike object or string representing an existing file

>   Filename of list of pre-defined TIs. Maps to a command-line argument: `-TIlist %s`.

> tr_valuea float

>   TR Repetition Time [10s!]. Maps to a command-line argument: `-TR %f` (position: 5).

> voxela tuple of the form: (an integer, an integer, an integer)

>   Fit to single voxel only. Maps to a command-line argument: `-voxel %d %d %d` (position: 10).

> comp_filea pathlike object or string representing a file

>   Filename of the estimated multi-component T1 map.

> error_filea pathlike object or string representing a file

>   Filename of the error map (symmetric matrix, [Diag,OffDiag]).

> m0map_filea pathlike object or string representing a file

>   Filename of the m0 map.

> mcmap_filea pathlike object or string representing a file

>   Filename of the estimated output multi-parameter map.

> res_filea pathlike object or string representing a file

>   Filename of the model fit residuals.

> syn_filea pathlike object or string representing a file

>   Filename of the synthetic ASL data.

> t1map_filea pathlike object or string representing a file

>   Filename of the estimated output T1 map (in ms).