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'
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).