nipype.interfaces.niftyfit.dwi module¶
The dwi module of niftyfit, which wraps the fitting methods in NiftyFit.
DwiTool¶
Bases: NiftyFitCommand
Wrapped executable:
dwi_tool
.Interface for executable dwi_tool from Niftyfit platform.
Use DwiTool.
Diffusion-Weighted MR Prediction. Predicts DWI from previously fitted models and calculates model derived maps.
Examples
>>> from nipype.interfaces import niftyfit >>> dwi_tool = niftyfit.DwiTool(dti_flag=True) >>> dwi_tool.inputs.source_file = 'dwi.nii.gz' >>> dwi_tool.inputs.bvec_file = 'bvecs' >>> dwi_tool.inputs.bval_file = 'bvals' >>> dwi_tool.inputs.mask_file = 'mask.nii.gz' >>> dwi_tool.inputs.b0_file = 'b0.nii.gz' >>> dwi_tool.inputs.rgbmap_file = 'rgb_map.nii.gz' >>> dwi_tool.cmdline 'dwi_tool -source dwi.nii.gz -bval bvals -bvec bvecs -b0 b0.nii.gz -mask mask.nii.gz -dti -famap dwi_famap.nii.gz -logdti2 dwi_logdti2.nii.gz -mcmap dwi_mcmap.nii.gz -mdmap dwi_mdmap.nii.gz -rgbmap rgb_map.nii.gz -syn dwi_syn.nii.gz -v1map dwi_v1map.nii.gz'
- bval_filea pathlike object or string representing an existing file
The file containing the bvalues of the source DWI. Maps to a command-line argument:
-bval %s
(position: 2).- source_filea pathlike object or string representing an existing file
The source image containing the fitted model. Maps to a command-line argument:
-source %s
(position: 1).
- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- b0_filea pathlike object or string representing an existing file
The B0 image corresponding to the source DWI. Maps to a command-line argument:
-b0 %s
(position: 4).- ball_flaga boolean
Input is a ball and stick model. Maps to a command-line argument:
-ball
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,dti_flag2
,ballv_flag
,nod_flag
,nodv_flag
.- ballv_flaga boolean
Input is a ball and stick model with optimised PDD. Maps to a command-line argument:
-ballv
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,dti_flag2
,ball_flag
,nod_flag
,nodv_flag
.- bvec_filea pathlike object or string representing an existing file
The file containing the bvectors of the source DWI. Maps to a command-line argument:
-bvec %s
(position: 3).- diso_vala float
Isotropic diffusivity for -nod [3e-3]. Maps to a command-line argument:
-diso %f
.- dpr_vala float
Parallel diffusivity for -nod [1.7e-3]. Maps to a command-line argument:
-dpr %f
.- dti_flaga boolean
Input is a tensor model diag/off-diag. Maps to a command-line argument:
-dti
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag2
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- dti_flag2a boolean
Input is a tensor model lower triangular. Maps to a command-line argument:
-dti2
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- 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:
{}
)- famap_filea pathlike object or string representing a file
Filename of FA map. Maps to a command-line argument:
-famap %s
.- ivim_flaga boolean
Inputs is an IVIM model to non-directional data. Maps to a command-line argument:
-ivim
(position: 6). Mutually exclusive with inputs:mono_flag
,dti_flag
,dti_flag2
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- logdti_filea pathlike object or string representing a file
Filename of output logdti map. Maps to a command-line argument:
-logdti2 %s
.- mask_filea pathlike object or string representing an existing file
The image mask. Maps to a command-line argument:
-mask %s
(position: 5).- mcmap_filea pathlike object or string representing a file
Filename of multi-compartment model parameter map (-ivim,-ball,-nod). Maps to a command-line argument:
-mcmap %s
.- mdmap_filea pathlike object or string representing a file
Filename of MD map/ADC. Maps to a command-line argument:
-mdmap %s
.- mono_flaga boolean
Input is a single exponential to non-directional data [default with no b-vectors]. Maps to a command-line argument:
-mono
(position: 6). Mutually exclusive with inputs:ivim_flag
,dti_flag
,dti_flag2
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- nod_flaga boolean
Input is a NODDI model. Maps to a command-line argument:
-nod
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,dti_flag2
,ball_flag
,ballv_flag
,nodv_flag
.- nodv_flaga boolean
Input is a NODDI model with optimised PDD. Maps to a command-line argument:
-nodv
(position: 6). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,dti_flag2
,ball_flag
,ballv_flag
,nod_flag
.- rgbmap_filea pathlike object or string representing a file
Filename of colour FA map. Maps to a command-line argument:
-rgbmap %s
.- syn_filea pathlike object or string representing a file
Filename of synthetic image. Requires: bvec_file/b0_file. Maps to a command-line argument:
-syn %s
. Requires inputs:bvec_file
,b0_file
.- v1map_filea pathlike object or string representing a file
Filename of PDD map [x,y,z]. Maps to a command-line argument:
-v1map %s
.
- famap_filea pathlike object or string representing a file
Filename of FA map.
- logdti_filea pathlike object or string representing a file
Filename of output logdti map.
- mcmap_filea pathlike object or string representing a file
Filename of multi-compartment model parameter map (-ivim,-ball,-nod).
- mdmap_filea pathlike object or string representing a file
Filename of MD map/ADC.
- rgbmap_filea pathlike object or string representing a file
Filename of colour FA map.
- syn_filea pathlike object or string representing a file
Filename of synthetic image.
- v1map_filea pathlike object or string representing a file
Filename of PDD map [x,y,z].
FitDwi¶
Bases: NiftyFitCommand
Wrapped executable:
fit_dwi
.Interface for executable fit_dwi from Niftyfit platform.
Use NiftyFit to perform diffusion model fitting.
Diffusion-weighted MR Fitting. Fits DWI parameter maps to multi-shell, multi-directional data.
Examples
>>> from nipype.interfaces import niftyfit >>> fit_dwi = niftyfit.FitDwi(dti_flag=True) >>> fit_dwi.inputs.source_file = 'dwi.nii.gz' >>> fit_dwi.inputs.bvec_file = 'bvecs' >>> fit_dwi.inputs.bval_file = 'bvals' >>> fit_dwi.inputs.rgbmap_file = 'rgb.nii.gz' >>> fit_dwi.cmdline 'fit_dwi -source dwi.nii.gz -bval bvals -bvec bvecs -dti -error dwi_error.nii.gz -famap dwi_famap.nii.gz -mcout dwi_mcout.txt -mdmap dwi_mdmap.nii.gz -nodiff dwi_no_diff.nii.gz -res dwi_resmap.nii.gz -rgbmap rgb.nii.gz -syn dwi_syn.nii.gz -tenmap2 dwi_tenmap2.nii.gz -v1map dwi_v1map.nii.gz'
- bval_filea pathlike object or string representing an existing file
The file containing the bvalues of the source DWI. Maps to a command-line argument:
-bval %s
(position: 2).- bvec_filea pathlike object or string representing an existing file
The file containing the bvectors of the source DWI. Maps to a command-line argument:
-bvec %s
(position: 3).- source_filea pathlike object or string representing an existing file
The source image containing the dwi data. 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:
-accpetance %f
.- argsa string
Additional parameters to the command. Maps to a command-line argument:
%s
.- ball_flaga boolean
Fit the ball and stick model. Maps to a command-line argument:
-ball
(position: 4). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,ballv_flag
,nod_flag
,nodv_flag
.- ballv_flaga boolean
Fit the ball and stick model with optimised PDD. Maps to a command-line argument:
-ballv
(position: 4). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,ball_flag
,nod_flag
,nodv_flag
.- cov_filea pathlike object or string representing an existing file
Filename of ithe nc*nc covariance matrix [I]. Maps to a command-line argument:
-cov %s
.- csf_t2_vala float
CSF T2 value [400ms]. Maps to a command-line argument:
-csfT2 %f
.- diso_vala float
Isotropic diffusivity for -nod [3e-3]. Maps to a command-line argument:
-diso %f
.- dpr_vala float
Parallel diffusivity for -nod [1.7e-3]. Maps to a command-line argument:
-dpr %f
.- dti_flaga boolean
Fit the tensor model [default with b-vectors]. Maps to a command-line argument:
-dti
(position: 4). Mutually exclusive with inputs:mono_flag
,ivim_flag
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- 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 parameter error maps. Maps to a command-line argument:
-error %s
.- famap_filea pathlike object or string representing a file
Filename of FA map. Maps to a command-line argument:
-famap %s
.- gn_flaga boolean
Use Gauss-Newton algorithm [Levenberg-Marquardt]. Maps to a command-line argument:
-gn
. Mutually exclusive with inputs:wls_flag
.- ivim_flaga boolean
Fit IVIM model to non-directional data. Maps to a command-line argument:
-ivim
(position: 4). Mutually exclusive with inputs:mono_flag
,dti_flag
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- lm_valsa tuple of the form: (a float, a float)
LM parameters (initial value, decrease rate) [100,1.2]. Maps to a command-line argument:
-lm %f %f
. Requires inputs:gn_flag
.- mask_filea pathlike object or string representing an existing file
The image mask. Maps to a command-line argument:
-mask %s
.- maxit_valan integer
Maximum number of non-linear LSQR iterations [100x2 passes]). Maps to a command-line argument:
-maxit %d
. Requires inputs:gn_flag
.- mcmap_filea pathlike object or string representing a file
Filename of multi-compartment model parameter map (-ivim,-ball,-nod). Maps to a command-line argument:
-mcmap %s
. Requires inputs:nodv_flag
.- mcmaxitan integer
Number of iterations to run [10,000]. Maps to a command-line argument:
-mcmaxit %d
.- mcouta pathlike object or string representing a 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
.- mdmap_filea pathlike object or string representing a file
Filename of MD map/ADC. Maps to a command-line argument:
-mdmap %s
.- mono_flaga boolean
Fit single exponential to non-directional data [default with no b-vectors]. Maps to a command-line argument:
-mono
(position: 4). Mutually exclusive with inputs:ivim_flag
,dti_flag
,ball_flag
,ballv_flag
,nod_flag
,nodv_flag
.- nod_flaga boolean
Fit the NODDI model. Maps to a command-line argument:
-nod
(position: 4). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,ball_flag
,ballv_flag
,nodv_flag
.- nodiff_filea pathlike object or string representing a file
Filename of average no diffusion image. Maps to a command-line argument:
-nodiff %s
.- nodv_flaga boolean
Fit the NODDI model with optimised PDD. Maps to a command-line argument:
-nodv
(position: 4). Mutually exclusive with inputs:mono_flag
,ivim_flag
,dti_flag
,ball_flag
,ballv_flag
,nod_flag
.- perf_thra float
Threshold for perfusion/diffsuion effects [100]. Maps to a command-line argument:
-perfthreshold %f
.- prior_filea pathlike object or string representing an existing file
Filename of parameter priors for -ball and -nod. Maps to a command-line argument:
-prior %s
.- res_filea pathlike object or string representing a file
Filename of model residual map. Maps to a command-line argument:
-res %s
.- rgbmap_filea pathlike object or string representing a file
Filename of colour-coded FA map. Maps to a command-line argument:
-rgbmap %s
. Requires inputs:dti_flag
.- rot_sform_flagan integer
Rotate the output tensors according to the q/s form of the image (resulting tensors will be in mm coordinates, default: 0). Maps to a command-line argument:
-rotsform %d
.- slice_noan integer
Fit to single slice number. Maps to a command-line argument:
-slice %d
.- swls_vala float
Use location-weighted least squares for DTI fitting [3x3 Gaussian]. Maps to a command-line argument:
-swls %f
.- syn_filea pathlike object or string representing a file
Filename of synthetic image. Maps to a command-line argument:
-syn %s
.- te_filea pathlike object or string representing an existing file
Filename of TEs (ms). Maps to a command-line argument:
-TE %s
. Mutually exclusive with inputs:te_file
.- te_valuea pathlike object or string representing an existing file
Value of TEs (ms). Maps to a command-line argument:
-TE %s
. Mutually exclusive with inputs:te_file
.- ten_type‘lower-tri’ or ‘diag-off-diag’
Use lower triangular (tenmap2) or diagonal, off-diagonal tensor format. (Nipype default value:
lower-tri
)- tenmap2_filea pathlike object or string representing a file
Filename of tensor map [lower tri]. Maps to a command-line argument:
-tenmap2 %s
. Requires inputs:dti_flag
.- tenmap_filea pathlike object or string representing a file
Filename of tensor map [diag,offdiag]. Maps to a command-line argument:
-tenmap %s
. Requires inputs:dti_flag
.- v1map_filea pathlike object or string representing a file
Filename of PDD map [x,y,z]. Maps to a command-line argument:
-v1map %s
.- vb_flaga boolean
Use Variational Bayes fitting with known prior (currently identity covariance…). Maps to a command-line argument:
-vb
.- 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
.- wls_flaga boolean
Use Variational Bayes fitting with known prior (currently identity covariance…). Maps to a command-line argument:
-wls
. Mutually exclusive with inputs:gn_flag
.- wm_t2_vala float
White matter T2 value [80ms]. Maps to a command-line argument:
-wmT2 %f
.
- error_filea pathlike object or string representing a file
Filename of parameter error maps.
- famap_filea pathlike object or string representing a file
Filename of FA map.
- mcmap_filea pathlike object or string representing a file
Filename of multi-compartment model parameter map (-ivim,-ball,-nod).
- mcouta pathlike object or string representing a file
Filename of mc samples (ascii text file).
- mdmap_filea pathlike object or string representing a file
Filename of MD map/ADC.
- nodiff_filea pathlike object or string representing a file
Filename of average no diffusion image.
- res_filea pathlike object or string representing a file
Filename of model residual map.
- rgbmap_filea pathlike object or string representing a file
Filename of colour FA map.
- syn_filea pathlike object or string representing a file
Filename of synthetic image.
- tenmap2_filea pathlike object or string representing a file
Filename of tensor map [lower tri].
- tenmap_filea pathlike object or string representing a file
Filename of tensor map.
- v1map_filea pathlike object or string representing a file
Filename of PDD map [x,y,z].