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'
- Mandatory Inputs:
source_file (a 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).- Optional Inputs:
acceptance (a float) – Fraction of iterations to accept [0.23]. Maps to a command-line argument:
-acceptance %f
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.b1map (a 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_file (a pathlike object or string representing a file) – Filename of the estimated multi-component T1 map. Maps to a command-line argument:
-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’) – Environment variables. (Nipype default value:
{}
)error_file (a pathlike object or string representing a file) – Filename of the error map (symmetric matrix, [Diag,OffDiag]). Maps to a command-line argument:
-error %s
.flips (a list of items which are a float) – Flip angles. Maps to a command-line argument:
-flips %s
.flips_list (a 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_flag (a boolean) – Use Gauss-Newton algorithm [Levenberg-Marquardt]. Maps to a command-line argument:
-gn
(position: 8).ir_flag (a boolean) – Inversion Recovery fitting [default]. Maps to a command-line 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]. Maps to a command-line argument:
-lm %f %f
(position: 7).m0map_file (a pathlike object or string representing a file) – Filename of the estimated input M0 map. Maps to a command-line argument:
-m0map %s
.mask (a pathlike object or string representing an existing file) – Filename of image mask. Maps to a command-line argument:
-mask %s
(position: 2).maxit (an integer) – NLSQR iterations [100]. Maps to a command-line argument:
-maxit %d
(position: 11).mcmap_file (a pathlike object or string representing a file) – Filename of the estimated output multi-parameter map. Maps to a command-line argument:
-mcmap %s
.mcmaxit (an integer) – Number of iterations to run [10,000]. Maps to a command-line argument:
-mcmaxit %d
.mcout (a pathlike object or string representing an existing file) – Filename of mc samples (ascii text file). Maps to a command-line argument:
-mcout %s
.mcsamples (an integer) – Number of samples to keep [100]. Maps to a command-line argument:
-mcsamples %d
.nb_comp (an integer) – Number of components to fit [1] (currently IR/SR only). Maps to a command-line argument:
-nc %d
(position: 6).prior (a pathlike object or string representing an existing file) – Filename of parameter prior. Maps to a command-line argument:
-prior %s
(position: 3).res_file (a pathlike object or string representing a file) – Filename of the model fit residuals. Maps to a command-line argument:
-res %s
.slice_no (an integer) – Fit to single slice number. Maps to a command-line argument:
-slice %d
(position: 9).spgr (a boolean) – Spoiled Gradient Echo fitting. Maps to a command-line argument:
-SPGR
.sr_flag (a boolean) – Saturation Recovery fitting [default]. Maps to a command-line argument:
-SR
(position: 12).syn_file (a pathlike object or string representing a file) – Filename of the synthetic ASL data. Maps to a command-line argument:
-syn %s
.t1_list (a pathlike object or string representing an existing file) – Filename of list of pre-defined T1s. Maps to a command-line argument:
-T1list %s
.t1map_file (a pathlike object or string representing a file) – Filename of the estimated output T1 map (in ms). Maps to a command-line argument:
-t1map %s
.t1max (a float) – Maximum tissue T1 value [4000ms]. Maps to a command-line argument:
-T1max %f
.t1min (a float) – Minimum tissue T1 value [400ms]. Maps to a command-line argument:
-T1min %f
.te_value (a float) – TE Echo Time [0ms!]. Maps to a command-line argument:
-TE %f
(position: 4).tis (a 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_list (a pathlike object or string representing an existing file) – Filename of list of pre-defined TIs. Maps to a command-line argument:
-TIlist %s
.tr_value (a float) – TR Repetition Time [10s!]. Maps to a command-line argument:
-TR %f
(position: 5).voxel (a 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).- Outputs:
comp_file (a pathlike object or string representing a file) – Filename of the estimated multi-component T1 map.
error_file (a pathlike object or string representing a file) – Filename of the error map (symmetric matrix, [Diag,OffDiag]).
m0map_file (a pathlike object or string representing a file) – Filename of the m0 map.
mcmap_file (a pathlike object or string representing a file) – Filename of the estimated output multi-parameter map.
res_file (a pathlike object or string representing a file) – Filename of the model fit residuals.
syn_file (a pathlike object or string representing a file) – Filename of the synthetic ASL data.
t1map_file (a pathlike object or string representing a file) – Filename of the estimated output T1 map (in ms).