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).