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'
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

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'
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].