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 bytes or None or a value
         of class 'str' and with values which are a bytes or None or a value
         of class 'str', 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: ('stream' or 'allatonce' or 'file' or '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)