interfaces.niftyfit.qt1

FitQt1

Link to code

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

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