interfaces.niftyfit.qt1¶
FitQt1¶
Wraps 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.
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.
flag: -source %s, position: 1
[Optional]
acceptance: (a float)
Fraction of iterations to accept [0.23].
flag: -acceptance %f
args: (a unicode string)
Additional parameters to the command
flag: %s
b1map: (a file name)
Filename of B1 estimate for fitting (or include in prior).
flag: -b1map %s
comp_file: (a file name)
Filename of the estimated multi-component T1 map.
flag: -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', nipype default value: {})
Environment variables
error_file: (a file name)
Filename of the error map (symmetric matrix, [Diag,OffDiag]).
flag: -error %s
flips: (a list of items which are a float)
Flip angles
flag: -flips %s
flips_list: (a file name)
Filename of list of pre-defined flip angles (deg).
flag: -fliplist %s
gn_flag: (a boolean)
Use Gauss-Newton algorithm [Levenberg-Marquardt].
flag: -gn, position: 8
ignore_exception: (a boolean, nipype default value: False)
Print an error message instead of throwing an exception in case the
interface fails to run
ir_flag: (a boolean)
Inversion Recovery fitting [default].
flag: -IR, position: 13
lm_val: (a tuple of the form: (a float, a float))
Set LM parameters (initial value, decrease rate) [100,1.2].
flag: -lm %f %f, position: 7
m0map_file: (a file name)
Filename of the estimated input M0 map.
flag: -m0map %s
mask: (an existing file name)
Filename of image mask.
flag: -mask %s, position: 2
maxit: (an integer (int or long))
NLSQR iterations [100].
flag: -maxit %d, position: 11
mcmap_file: (a file name)
Filename of the estimated output multi-parameter map.
flag: -mcmap %s
mcmaxit: (an integer (int or long))
Number of iterations to run [10,000].
flag: -mcmaxit %d
mcout: (a file name)
Filename of mc samples (ascii text file)
flag: -mcout %s
mcsamples: (an integer (int or long))
Number of samples to keep [100].
flag: -mcsamples %d
nb_comp: (an integer (int or long))
Number of components to fit [1] (currently IR/SR only)
flag: -nc %d, position: 6
prior: (an existing file name)
Filename of parameter prior.
flag: -prior %s, position: 3
res_file: (a file name)
Filename of the model fit residuals
flag: -res %s
slice_no: (an integer (int or long))
Fit to single slice number.
flag: -slice %d, position: 9
spgr: (a boolean)
Spoiled Gradient Echo fitting
flag: -SPGR
sr_flag: (a boolean)
Saturation Recovery fitting [default].
flag: -SR, position: 12
syn_file: (a file name)
Filename of the synthetic ASL data.
flag: -syn %s
t1_list: (a file name)
Filename of list of pre-defined T1s
flag: -T1list %s
t1map_file: (a file name)
Filename of the estimated output T1 map (in ms).
flag: -t1map %s
t1max: (a float)
Maximum tissue T1 value [4000ms].
flag: -T1max %f
t1min: (a float)
Minimum tissue T1 value [400ms].
flag: -T1min %f
te_value: (a float)
TE Echo Time [0ms!].
flag: -TE %f, position: 4
terminal_output: ('stream' or 'allatonce' or 'file' or 'none')
Control terminal output: `stream` - displays to terminal immediately
(default), `allatonce` - waits till command is finished to display
output, `file` - writes output to file, `none` - output is ignored
tis: (a list of items which are a float)
Inversion times for T1 data [1s,2s,5s].
flag: -TIs %s, position: 14
tis_list: (a file name)
Filename of list of pre-defined TIs.
flag: -TIlist %s
tr_value: (a float)
TR Repetition Time [10s!].
flag: -TR %f, position: 5
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.
flag: -voxel %d %d %d, position: 10
Outputs:
comp_file: (a file name)
Filename of the estimated multi-component T1 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
mcmap_file: (a file name)
Filename of the estimated output multi-parameter map
res_file: (a file name)
Filename of the model fit residuals
syn_file: (a file name)
Filename of the synthetic ASL data
t1map_file: (a file name)
Filename of the estimated output T1 map (in ms)