nipype.interfaces.niftyfit.qt1 module¶
The QT1 module of niftyfit, which wraps the Multi-Echo T1 fitting methods in NiftyFit.
FitQt1¶
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.
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 unicode 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 (int or long)
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 (int or long)
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 (int or long)
Number of samples to keep [100]. Maps to a command-line argument:
-mcsamples %d
.- nb_compan integer (int or long)
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 (int or long)
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 (int or long), an integer (int or long), an integer (int or long))
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).