nipype.interfaces.niftyfit.dwi module

The dwi module of niftyfit, which wraps the fitting methods in NiftyFit.

DwiTool

Link to code

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.

Source code

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_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).
args : a unicode 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.
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

Link to code

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.

Source code

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_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).
acceptance : a float
Fraction of iterations to accept [0.23]. Maps to a command-line argument: -accpetance %f.
args : a unicode 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 (int or long)
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 (int or long)
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 (int or long)
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 (int or long)
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 (int or long)
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 (int or long), an integer (int or long), an integer (int or long))
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.
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].