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'
- Mandatory Inputs:
bval_file (a 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_file (a 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).- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.b0_file (a 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_flag (a 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_flag (a 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_file (a 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_val (a float) – Isotropic diffusivity for -nod [3e-3]. Maps to a command-line argument:
-diso %f
.dpr_val (a float) – Parallel diffusivity for -nod [1.7e-3]. Maps to a command-line argument:
-dpr %f
.dti_flag (a 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_flag2 (a 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
.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:
{}
)famap_file (a pathlike object or string representing a file) – Filename of FA map. Maps to a command-line argument:
-famap %s
.ivim_flag (a 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_file (a pathlike object or string representing a file) – Filename of output logdti map. Maps to a command-line argument:
-logdti2 %s
.mask_file (a pathlike object or string representing an existing file) – The image mask. Maps to a command-line argument:
-mask %s
(position: 5).mcmap_file (a 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_file (a pathlike object or string representing a file) – Filename of MD map/ADC. Maps to a command-line argument:
-mdmap %s
.mono_flag (a 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_flag (a 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_flag (a 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_file (a pathlike object or string representing a file) – Filename of colour FA map. Maps to a command-line argument:
-rgbmap %s
.syn_file (a 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_file (a pathlike object or string representing a file) – Filename of PDD map [x,y,z]. Maps to a command-line argument:
-v1map %s
.- Outputs:
famap_file (a pathlike object or string representing a file) – Filename of FA map.
logdti_file (a pathlike object or string representing a file) – Filename of output logdti map.
mcmap_file (a pathlike object or string representing a file) – Filename of multi-compartment model parameter map (-ivim,-ball,-nod).
mdmap_file (a pathlike object or string representing a file) – Filename of MD map/ADC.
rgbmap_file (a pathlike object or string representing a file) – Filename of colour FA map.
syn_file (a pathlike object or string representing a file) – Filename of synthetic image.
v1map_file (a 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'
- Mandatory Inputs:
bval_file (a 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_file (a 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_file (a 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).- Optional Inputs:
acceptance (a float) – Fraction of iterations to accept [0.23]. Maps to a command-line argument:
-accpetance %f
.args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s
.ball_flag (a 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_flag (a 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_file (a 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_val (a float) – CSF T2 value [400ms]. Maps to a command-line argument:
-csfT2 %f
.diso_val (a float) – Isotropic diffusivity for -nod [3e-3]. Maps to a command-line argument:
-diso %f
.dpr_val (a float) – Parallel diffusivity for -nod [1.7e-3]. Maps to a command-line argument:
-dpr %f
.dti_flag (a 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
.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 parameter error maps. Maps to a command-line argument:
-error %s
.famap_file (a pathlike object or string representing a file) – Filename of FA map. Maps to a command-line argument:
-famap %s
.gn_flag (a boolean) – Use Gauss-Newton algorithm [Levenberg-Marquardt]. Maps to a command-line argument:
-gn
. Mutually exclusive with inputs:wls_flag
.ivim_flag (a 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_vals (a 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_file (a pathlike object or string representing an existing file) – The image mask. Maps to a command-line argument:
-mask %s
.maxit_val (an integer) – Maximum number of non-linear LSQR iterations [100x2 passes]). Maps to a command-line argument:
-maxit %d
. Requires inputs:gn_flag
.mcmap_file (a 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
.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 a 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
.mdmap_file (a pathlike object or string representing a file) – Filename of MD map/ADC. Maps to a command-line argument:
-mdmap %s
.mono_flag (a 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_flag (a 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_file (a pathlike object or string representing a file) – Filename of average no diffusion image. Maps to a command-line argument:
-nodiff %s
.nodv_flag (a 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_thr (a float) – Threshold for perfusion/diffsuion effects [100]. Maps to a command-line argument:
-perfthreshold %f
.prior_file (a 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_file (a pathlike object or string representing a file) – Filename of model residual map. Maps to a command-line argument:
-res %s
.rgbmap_file (a 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_flag (an 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_no (an integer) – Fit to single slice number. Maps to a command-line argument:
-slice %d
.swls_val (a float) – Use location-weighted least squares for DTI fitting [3x3 Gaussian]. Maps to a command-line argument:
-swls %f
.syn_file (a pathlike object or string representing a file) – Filename of synthetic image. Maps to a command-line argument:
-syn %s
.te_file (a 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_value (a 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_file (a 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_file (a 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_file (a pathlike object or string representing a file) – Filename of PDD map [x,y,z]. Maps to a command-line argument:
-v1map %s
.vb_flag (a boolean) – Use Variational Bayes fitting with known prior (currently identity covariance…). Maps to a command-line argument:
-vb
.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
.wls_flag (a 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_val (a float) – White matter T2 value [80ms]. Maps to a command-line argument:
-wmT2 %f
.- Outputs:
error_file (a pathlike object or string representing a file) – Filename of parameter error maps.
famap_file (a pathlike object or string representing a file) – Filename of FA map.
mcmap_file (a pathlike object or string representing a file) – Filename of multi-compartment model parameter map (-ivim,-ball,-nod).
mcout (a pathlike object or string representing a file) – Filename of mc samples (ascii text file).
mdmap_file (a pathlike object or string representing a file) – Filename of MD map/ADC.
nodiff_file (a pathlike object or string representing a file) – Filename of average no diffusion image.
res_file (a pathlike object or string representing a file) – Filename of model residual map.
rgbmap_file (a pathlike object or string representing a file) – Filename of colour FA map.
syn_file (a pathlike object or string representing a file) – Filename of synthetic image.
tenmap2_file (a pathlike object or string representing a file) – Filename of tensor map [lower tri].
tenmap_file (a pathlike object or string representing a file) – Filename of tensor map.
v1map_file (a pathlike object or string representing a file) – Filename of PDD map [x,y,z].