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# nipype.interfaces.fsl.dti module

The fsl module provides classes for interfacing with the FSL command line tools. This was written to work with FSL version 4.1.4.

## BEDPOSTX

Link to code

> alias of `nipype.interfaces.fsl.dti.BEDPOSTX5`

## BEDPOSTX5

Link to code

> Bases: FSLXCommand

> Wrapped executable: `bedpostx`.

> BEDPOSTX stands for Bayesian Estimation of Diffusion Parameters Obtained using Sampling Techniques. The X stands for modelling Crossing Fibres. bedpostx runs Markov Chain Monte Carlo sampling to build up distributions on diffusion parameters at each voxel. It creates all the files necessary for running probabilistic tractography. For an overview of the modelling carried out within bedpostx see this technical report.

> Note

> Consider using `niflow.nipype1.workflows.fsl.dmri.create_bedpostx_pipeline()` instead.

> Example

>     >>> from nipype.interfaces import fsl
>     >>> bedp = fsl.BEDPOSTX5(bvecs='bvecs', bvals='bvals', dwi='diffusion.nii',
>     ...                     mask='mask.nii', n_fibres=1)
>     >>> bedp.cmdline
>     'bedpostx bedpostx -b 0 --burnin_noard=0 --forcedir -n 1 -j 5000 -s 1 --updateproposalevery=40'

> bvalsa pathlike object or string representing an existing file

>   B values file.

> bvecsa pathlike object or string representing an existing file

>   B vectors file.

> dwia pathlike object or string representing an existing file

>   Diffusion weighted image data file.

> maska pathlike object or string representing an existing file

>   Bet binary mask file.

> n_fibresa long integer >= 1

>   Maximum number of fibres to fit in each voxel. Maps to a command-line argument: `-n %d`. (Nipype default value: `2`)

> out_dira pathlike object or string representing a directory

>   Output directory. Maps to a command-line argument: `%s` (position: 1). (Nipype default value: `bedpostx`)

> all_arda boolean

>   Turn ARD on on all fibres. Maps to a command-line argument: `--allard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> burn_ina long integer >= 0

>   Total num of jumps at start of MCMC to be discarded. Maps to a command-line argument: `-b %d`. (Nipype default value: `0`)

> burn_in_no_arda long integer >= 0

>   Num of burnin jumps before the ard is imposed. Maps to a command-line argument: `--burnin_noard=%d`. (Nipype default value: `0`)

> cnlineara boolean

>   Initialise with constrained nonlinear fitting. Maps to a command-line argument: `--cnonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> 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: `{}`)

> f0_arda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0 --ardf0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`, `all_ard`.

> f0_noarda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`.

> force_dira boolean

>   Use the actual directory name given (do not add + to make a new directory). Maps to a command-line argument: `--forcedir`. (Nipype default value: `True`)

> fudgean integer (int or long)

>   ARD fudge factor. Maps to a command-line argument: `-w %d`.

> grad_deva pathlike object or string representing an existing file

>   Grad_dev file, if gradnonlin, -g is True.

> gradnonlina boolean

>   Consider gradient nonlinearities, default off. Maps to a command-line argument: `-g`.

> logdira pathlike object or string representing a directory

>   Maps to a command-line argument: `--logdir=%s`.

> model1 or 2 or 3

>   Use monoexponential (1, default, required for single-shell) or multiexponential (2, multi-shell) model. Maps to a command-line argument: `-model %d`.

> n_jumpsan integer (int or long)

>   Num of jumps to be made by MCMC. Maps to a command-line argument: `-j %d`. (Nipype default value: `5000`)

> no_arda boolean

>   Turn ARD off on all fibres. Maps to a command-line argument: `--noard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> no_spata boolean

>   Initialise with tensor, not spatially. Maps to a command-line argument: `--nospat`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> non_lineara boolean

>   Initialise with nonlinear fitting. Maps to a command-line argument: `--nonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> riciana boolean

>   Use Rician noise modeling. Maps to a command-line argument: `--rician`.

> sample_everya long integer >= 0

>   Num of jumps for each sample (MCMC). Maps to a command-line argument: `-s %d`. (Nipype default value: `1`)

> seedan integer (int or long)

>   Seed for pseudo random number generator. Maps to a command-line argument: `--seed=%d`.

> update_proposal_everya long integer >= 1

>   Num of jumps for each update to the proposal density std (MCMC). Maps to a command-line argument: `--updateproposalevery=%d`. (Nipype default value: `40`)

> use_gpua boolean

>   Use the GPU version of bedpostx.

> dyadsa list of items which are a pathlike object or string representing an existing file

>   Mean of PDD distribution in vector form.

> dyads_dispersiona list of items which are a pathlike object or string representing an existing file

>   Dispersion.

> mean_S0samplesa pathlike object or string representing an existing file

>   Mean of distribution on T2wbaseline signal intensity S0.

> mean_dsamplesa pathlike object or string representing an existing file

>   Mean of distribution on diffusivity d.

> mean_fsamplesa list of items which are a pathlike object or string representing an existing file

>   Mean of distribution on f anisotropy.

> mean_phsamplesa list of items which are a pathlike object or string representing an existing file

>   Mean of distribution on phi.

> mean_thsamplesa list of items which are a pathlike object or string representing an existing file

>   Mean of distribution on theta.

> merged_fsamplesa list of items which are a pathlike object or string representing an existing file

>   Samples from the distribution on anisotropic volume fraction.

> merged_phsamplesa list of items which are a pathlike object or string representing an existing file

>   Samples from the distribution on phi.

> merged_thsamplesa list of items which are a pathlike object or string representing an existing file

>   Samples from the distribution on theta.

## DTIFit

Link to code

> Bases: FSLCommand

> Wrapped executable: `dtifit`.

> Use FSL dtifit command for fitting a diffusion tensor model at each voxel

> Example

>     >>> from nipype.interfaces import fsl
>     >>> dti = fsl.DTIFit()
>     >>> dti.inputs.dwi = 'diffusion.nii'
>     >>> dti.inputs.bvecs = 'bvecs'
>     >>> dti.inputs.bvals = 'bvals'
>     >>> dti.inputs.base_name = 'TP'
>     >>> dti.inputs.mask = 'mask.nii'
>     >>> dti.cmdline
>     'dtifit -k diffusion.nii -o TP -m mask.nii -r bvecs -b bvals'

> bvalsa pathlike object or string representing an existing file

>   B values file. Maps to a command-line argument: `-b %s` (position: 4).

> bvecsa pathlike object or string representing an existing file

>   B vectors file. Maps to a command-line argument: `-r %s` (position: 3).

> dwia pathlike object or string representing an existing file

>   Diffusion weighted image data file. Maps to a command-line argument: `-k %s` (position: 0).

> maska pathlike object or string representing an existing file

>   Bet binary mask file. Maps to a command-line argument: `-m %s` (position: 2).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> base_namea unicode string

>   Base_name that all output files will start with. Maps to a command-line argument: `-o %s` (position: 1). (Nipype default value: `dtifit_`)

> cnia pathlike object or string representing an existing file

>   Input counfound regressors. Maps to a command-line argument: `--cni=%s`.

> 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: `{}`)

> gradnonlina pathlike object or string representing an existing file

>   Gradient non linearities. Maps to a command-line argument: `--gradnonlin=%s`.

> little_bita boolean

>   Only process small area of brain. Maps to a command-line argument: `--littlebit`.

> max_xan integer (int or long)

>   Max x. Maps to a command-line argument: `-X %d`.

> max_yan integer (int or long)

>   Max y. Maps to a command-line argument: `-Y %d`.

> max_zan integer (int or long)

>   Max z. Maps to a command-line argument: `-Z %d`.

> min_xan integer (int or long)

>   Min x. Maps to a command-line argument: `-x %d`.

> min_yan integer (int or long)

>   Min y. Maps to a command-line argument: `-y %d`.

> min_zan integer (int or long)

>   Min z. Maps to a command-line argument: `-z %d`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> save_tensora boolean

>   Save the elements of the tensor. Maps to a command-line argument: `--save_tensor`.

> ssea boolean

>   Output sum of squared errors. Maps to a command-line argument: `--sse`.

> FAa pathlike object or string representing an existing file

>   Path/name of file with the fractional anisotropy.

> L1a pathlike object or string representing an existing file

>   Path/name of file with the 1st eigenvalue.

> L2a pathlike object or string representing an existing file

>   Path/name of file with the 2nd eigenvalue.

> L3a pathlike object or string representing an existing file

>   Path/name of file with the 3rd eigenvalue.

> MDa pathlike object or string representing an existing file

>   Path/name of file with the mean diffusivity.

> MOa pathlike object or string representing an existing file

>   Path/name of file with the mode of anisotropy.

> S0a pathlike object or string representing an existing file

>   Path/name of file with the raw T2 signal with no diffusion weighting.

> V1a pathlike object or string representing an existing file

>   Path/name of file with the 1st eigenvector.

> V2a pathlike object or string representing an existing file

>   Path/name of file with the 2nd eigenvector.

> V3a pathlike object or string representing an existing file

>   Path/name of file with the 3rd eigenvector.

> ssea pathlike object or string representing an existing file

>   Path/name of file with the summed squared error.

> tensora pathlike object or string representing an existing file

>   Path/name of file with the 4D tensor volume.

## DistanceMap

Link to code

> Bases: FSLCommand

> Wrapped executable: `distancemap`.

> Use FSL’s distancemap to generate a map of the distance to the nearest nonzero voxel.

> Example

>     >>> import nipype.interfaces.fsl as fsl
>     >>> mapper = fsl.DistanceMap()
>     >>> mapper.inputs.in_file = "skeleton_mask.nii.gz"
>     >>> mapper.run()

> in_filea pathlike object or string representing an existing file

>   Image to calculate distance values for. Maps to a command-line argument: `--in=%s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> distance_mapa pathlike object or string representing a file

>   Distance map to write. Maps to a command-line argument: `--out=%s`.

> 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: `{}`)

> invert_inputa boolean

>   Invert input image. Maps to a command-line argument: `--invert`.

> local_max_filea boolean or a pathlike object or string representing a file

>   Write an image of the local maxima. Maps to a command-line argument: `--localmax=%s`.

> mask_filea pathlike object or string representing an existing file

>   Binary mask to contrain calculations. Maps to a command-line argument: `--mask=%s`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> distance_mapa pathlike object or string representing an existing file

>   Value is distance to nearest nonzero voxels.

> local_max_filea pathlike object or string representing a file

>   Image of local maxima.

## FSLXCommand

Link to code

> Bases: FSLCommand

> Base support for `xfibres` and `bedpostx`

> bvalsa pathlike object or string representing an existing file

>   B values file. Maps to a command-line argument: `--bvals=%s`.

> bvecsa pathlike object or string representing an existing file

>   B vectors file. Maps to a command-line argument: `--bvecs=%s`.

> dwia pathlike object or string representing an existing file

>   Diffusion weighted image data file. Maps to a command-line argument: `--data=%s`.

> maska pathlike object or string representing an existing file

>   Brain binary mask file (i.e. from BET). Maps to a command-line argument: `--mask=%s`.

> n_fibresa long integer >= 1

>   Maximum number of fibres to fit in each voxel. Maps to a command-line argument: `--nfibres=%d`. (Nipype default value: `2`)

> all_arda boolean

>   Turn ARD on on all fibres. Maps to a command-line argument: `--allard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> burn_ina long integer >= 0

>   Total num of jumps at start of MCMC to be discarded. Maps to a command-line argument: `--burnin=%d`. (Nipype default value: `0`)

> burn_in_no_arda long integer >= 0

>   Num of burnin jumps before the ard is imposed. Maps to a command-line argument: `--burnin_noard=%d`. (Nipype default value: `0`)

> cnlineara boolean

>   Initialise with constrained nonlinear fitting. Maps to a command-line argument: `--cnonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> 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: `{}`)

> f0_arda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0 --ardf0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`, `all_ard`.

> f0_noarda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`.

> force_dira boolean

>   Use the actual directory name given (do not add + to make a new directory). Maps to a command-line argument: `--forcedir`. (Nipype default value: `True`)

> fudgean integer (int or long)

>   ARD fudge factor. Maps to a command-line argument: `--fudge=%d`.

> logdira pathlike object or string representing a directory

>   Maps to a command-line argument: `--logdir=%s`. (Nipype default value: `.`)

> model1 or 2 or 3

>   Use monoexponential (1, default, required for single-shell) or multiexponential (2, multi-shell) model. Maps to a command-line argument: `--model=%d`.

> n_jumpsan integer (int or long)

>   Num of jumps to be made by MCMC. Maps to a command-line argument: `--njumps=%d`. (Nipype default value: `5000`)

> no_arda boolean

>   Turn ARD off on all fibres. Maps to a command-line argument: `--noard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> no_spata boolean

>   Initialise with tensor, not spatially. Maps to a command-line argument: `--nospat`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> non_lineara boolean

>   Initialise with nonlinear fitting. Maps to a command-line argument: `--nonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> riciana boolean

>   Use Rician noise modeling. Maps to a command-line argument: `--rician`.

> sample_everya long integer >= 0

>   Num of jumps for each sample (MCMC). Maps to a command-line argument: `--sampleevery=%d`. (Nipype default value: `1`)

> seedan integer (int or long)

>   Seed for pseudo random number generator. Maps to a command-line argument: `--seed=%d`.

> update_proposal_everya long integer >= 1

>   Num of jumps for each update to the proposal density std (MCMC). Maps to a command-line argument: `--updateproposalevery=%d`. (Nipype default value: `40`)

> dyadsa list of items which are a pathlike object or string representing an existing file

>   Mean of PDD distribution in vector form.

> fsamplesa list of items which are a pathlike object or string representing an existing file

>   Samples from the distribution on f anisotropy.

> mean_S0samplesa pathlike object or string representing an existing file

>   Mean of distribution on T2wbaseline signal intensity S0.

> mean_dsamplesa pathlike object or string representing an existing file

>   Mean of distribution on diffusivity d.

> mean_fsamplesa list of items which are a pathlike object or string representing an existing file

>   Mean of distribution on f anisotropy.

> mean_tausamplesa pathlike object or string representing an existing file

>   Mean of distribution on tau samples (only with rician noise).

> phsamplesa list of items which are a pathlike object or string representing an existing file

>   Phi samples, per fiber.

> thsamplesa list of items which are a pathlike object or string representing an existing file

>   Theta samples, per fiber.

## FindTheBiggest

Link to code

> Bases: FSLCommand

> Wrapped executable: `find_the_biggest`.

> Use FSL find_the_biggest for performing hard segmentation on the outputs of connectivity-based thresholding in probtrack. For complete details, see the FDT Documentation.

> Example

>     >>> from nipype.interfaces import fsl
>     >>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii']
>     >>> fBig = fsl.FindTheBiggest(in_files=ldir, out_file='biggestSegmentation')
>     >>> fBig.cmdline
>     'find_the_biggest seeds_to_M1.nii seeds_to_M2.nii biggestSegmentation'

> in_filesa list of items which are a pathlike object or string representing an existing file

>   A list of input volumes or a singleMatrixFile. Maps to a command-line argument: `%s` (position: 0).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> 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: `{}`)

> out_filea pathlike object or string representing a file

>   File with the resulting segmentation. Maps to a command-line argument: `%s` (position: 2).

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filea pathlike object or string representing an existing file

>   Output file indexed in order of input files. Maps to a command-line argument: `%s`.

## MakeDyadicVectors

Link to code

> Bases: FSLCommand

> Wrapped executable: `make_dyadic_vectors`.

> Create vector volume representing mean principal diffusion direction and its uncertainty (dispersion)

> phi_vola pathlike object or string representing an existing file

>   Maps to a command-line argument: `%s` (position: 1).

> theta_vola pathlike object or string representing an existing file

>   Maps to a command-line argument: `%s` (position: 0).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> 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: `{}`)

> maska pathlike object or string representing an existing file

>   Maps to a command-line argument: `%s` (position: 2).

> outputa pathlike object or string representing a file

>   Maps to a command-line argument: `%s` (position: 3). (Nipype default value: `dyads`)

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> perca float

>   The {perc}% angle of the output cone of uncertainty (output will be in degrees). Maps to a command-line argument: `%f` (position: 4).

> dispersion : a pathlike object or string representing an existing file dyads : a pathlike object or string representing an existing file

## ProbTrackX

Link to code

> Bases: FSLCommand

> Wrapped executable: `probtrackx`.

> Use FSL probtrackx for tractography on bedpostx results

> Examples

>     >>> from nipype.interfaces import fsl
>     >>> pbx = fsl.ProbTrackX(samples_base_name='merged', mask='mask.nii',     seed='MASK_average_thal_right.nii', mode='seedmask',     xfm='trans.mat', n_samples=3, n_steps=10, force_dir=True, opd=True,     os2t=True, target_masks = ['targets_MASK1.nii', 'targets_MASK2.nii'],     thsamples='merged_thsamples.nii', fsamples='merged_fsamples.nii',     phsamples='merged_phsamples.nii', out_dir='.')
>     >>> pbx.cmdline
>     'probtrackx --forcedir -m mask.nii --mode=seedmask --nsamples=3 --nsteps=10 --opd --os2t --dir=. --samples=merged --seed=MASK_average_thal_right.nii --targetmasks=targets.txt --xfm=trans.mat'

> fsamples : a list of items which are a pathlike object or string representing an existing file mask : a pathlike object or string representing an existing file

> > Bet binary mask file in diffusion space. Maps to a command-line argument: `-m %s`.

> phsamples : a list of items which are a pathlike object or string representing an existing file seed : a pathlike object or string representing an existing file or a list of items which are a pathlike object or string representing an existing file or a list of items which are a list of from 3 to 3 items which are an integer (int or long)

> > Seed volume(s), or voxel(s) or freesurfer label file. Maps to a command-line argument: `--seed=%s`.

> thsamples : a list of items which are a pathlike object or string representing an existing file

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avoid_mpa pathlike object or string representing an existing file

>   Reject pathways passing through locations given by this mask. Maps to a command-line argument: `--avoid=%s`.

> c_thresha float

>   Curvature threshold - default=0.2. Maps to a command-line argument: `--cthr=%.3f`.

> correct_path_distributiona boolean

>   Correct path distribution for the length of the pathways. Maps to a command-line argument: `--pd`.

> dist_thresha float

>   Discards samples shorter than this threshold (in mm - default=0). Maps to a command-line argument: `--distthresh=%.3f`.

> 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: `{}`)

> fibstan integer (int or long)

>   Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0. Maps to a command-line argument: `--fibst=%d`.

> force_dira boolean

>   Use the actual directory name given - i.e. do not add + to make a new directory. Maps to a command-line argument: `--forcedir`. (Nipype default value: `True`)

> inv_xfma pathlike object or string representing a file

>   Transformation matrix taking DTI space to seed space (compulsory when using a warp_field for seeds_to_dti). Maps to a command-line argument: `--invxfm=%s`.

> loop_checka boolean

>   Perform loop_checks on paths - slower, but allows lower curvature threshold. Maps to a command-line argument: `--loopcheck`.

> mask2a pathlike object or string representing an existing file

>   Second bet binary mask (in diffusion space) in twomask_symm mode. Maps to a command-line argument: `--mask2=%s`.

> mesha pathlike object or string representing an existing file

>   Freesurfer-type surface descriptor (in ascii format). Maps to a command-line argument: `--mesh=%s`.

> mod_eulera boolean

>   Use modified euler streamlining. Maps to a command-line argument: `--modeuler`.

> mode‘simple’ or ‘two_mask_symm’ or ‘seedmask’

>   Options: simple (single seed voxel), seedmask (mask of seed voxels), twomask_symm (two bet binary masks). Maps to a command-line argument: `--mode=%s`.

> n_samplesan integer (int or long)

>   Number of samples - default=5000. Maps to a command-line argument: `--nsamples=%d`. (Nipype default value: `5000`)

> n_stepsan integer (int or long)

>   Number of steps per sample - default=2000. Maps to a command-line argument: `--nsteps=%d`.

> networka boolean

>   Activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks). Maps to a command-line argument: `--network`.

> opda boolean

>   Outputs path distributions. Maps to a command-line argument: `--opd`. (Nipype default value: `True`)

> os2ta boolean

>   Outputs seeds to targets. Maps to a command-line argument: `--os2t`.

> out_dira pathlike object or string representing an existing directory

>   Directory to put the final volumes in. Maps to a command-line argument: `--dir=%s`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> rand_fib0 or 1 or 2 or 3

>   Options: 0 - default, 1 - to randomly sample initial fibres (with f > fibthresh), 2 - to sample in proportion fibres (with f>fibthresh) to f, 3 - to sample ALL populations at random (even if f<fibthresh). Maps to a command-line argument: `--randfib=%d`.

> random_seeda boolean

>   Random seed. Maps to a command-line argument: `--rseed`.

> s2tastexta boolean

>   Output seed-to-target counts as a text file (useful when seeding from a mesh). Maps to a command-line argument: `--s2tastext`.

> sample_random_pointsa boolean

>   Sample random points within seed voxels. Maps to a command-line argument: `--sampvox`.

> samples_base_namea unicode string

>   The rootname/base_name for samples files. Maps to a command-line argument: `--samples=%s`. (Nipype default value: `merged`)

> seed_refa pathlike object or string representing an existing file

>   Reference vol to define seed space in simple mode - diffusion space assumed if absent. Maps to a command-line argument: `--seedref=%s`.

> step_lengtha float

>   Step_length in mm - default=0.5. Maps to a command-line argument: `--steplength=%.3f`.

> stop_maska pathlike object or string representing an existing file

>   Stop tracking at locations given by this mask file. Maps to a command-line argument: `--stop=%s`.

> target_masksa list of items which are a pathlike object or string representing a file

>   List of target masks - required for seeds_to_targets classification. Maps to a command-line argument: `--targetmasks=%s`.

> use_anisotropya boolean

>   Use anisotropy to constrain tracking. Maps to a command-line argument: `--usef`.

> verbose0 or 1 or 2

>   Verbose level, [0-2]. Level 2 is required to output particle files. Maps to a command-line argument: `--verbose=%d`.

> waypointsa pathlike object or string representing an existing file

>   Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks. Maps to a command-line argument: `--waypoints=%s`.

> xfma pathlike object or string representing an existing file

>   Transformation matrix taking seed space to DTI space (either FLIRT matrix or FNIRT warp_field) - default is identity. Maps to a command-line argument: `--xfm=%s`.

> fdt_pathsa list of items which are a pathlike object or string representing an existing file

>   Path/name of a 3D image file containing the output connectivity distribution to the seed mask.

> loga pathlike object or string representing an existing file

>   Path/name of a text record of the command that was run.

> particle_filesa list of items which are a pathlike object or string representing an existing file

>   Files describing all of the tract samples. Generated only if verbose is set to 2.

> targetsa list of items which are a pathlike object or string representing an existing file

>   A list with all generated seeds_to_target files.

> way_totala pathlike object or string representing an existing file

>   Path/name of a text file containing a single number corresponding to the total number of generated tracts that have not been rejected by inclusion/exclusion mask criteria.

## ProbTrackX2

Link to code

> Bases: ProbTrackX

> Wrapped executable: `probtrackx2`.

> Use FSL probtrackx2 for tractography on bedpostx results

> Examples

>     >>> from nipype.interfaces import fsl
>     >>> pbx2 = fsl.ProbTrackX2()
>     >>> pbx2.inputs.seed = 'seed_source.nii.gz'
>     >>> pbx2.inputs.thsamples = 'merged_th1samples.nii.gz'
>     >>> pbx2.inputs.fsamples = 'merged_f1samples.nii.gz'
>     >>> pbx2.inputs.phsamples = 'merged_ph1samples.nii.gz'
>     >>> pbx2.inputs.mask = 'nodif_brain_mask.nii.gz'
>     >>> pbx2.inputs.out_dir = '.'
>     >>> pbx2.inputs.n_samples = 3
>     >>> pbx2.inputs.n_steps = 10
>     >>> pbx2.cmdline
>     'probtrackx2 --forcedir -m nodif_brain_mask.nii.gz --nsamples=3 --nsteps=10 --opd --dir=. --samples=merged --seed=seed_source.nii.gz'

> fsamples : a list of items which are a pathlike object or string representing an existing file mask : a pathlike object or string representing an existing file

> > Bet binary mask file in diffusion space. Maps to a command-line argument: `-m %s`.

> phsamples : a list of items which are a pathlike object or string representing an existing file seed : a pathlike object or string representing an existing file or a list of items which are a pathlike object or string representing an existing file or a list of items which are a list of from 3 to 3 items which are an integer (int or long)

> > Seed volume(s), or voxel(s) or freesurfer label file. Maps to a command-line argument: `--seed=%s`.

> thsamples : a list of items which are a pathlike object or string representing an existing file

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> avoid_mpa pathlike object or string representing an existing file

>   Reject pathways passing through locations given by this mask. Maps to a command-line argument: `--avoid=%s`.

> c_thresha float

>   Curvature threshold - default=0.2. Maps to a command-line argument: `--cthr=%.3f`.

> colmask4a pathlike object or string representing an existing file

>   Mask for columns of matrix4 (default=seed mask). Maps to a command-line argument: `--colmask4=%s`.

> correct_path_distributiona boolean

>   Correct path distribution for the length of the pathways. Maps to a command-line argument: `--pd`.

> dist_thresha float

>   Discards samples shorter than this threshold (in mm - default=0). Maps to a command-line argument: `--distthresh=%.3f`.

> distthresh1a float

>   Discards samples (in matrix1) shorter than this threshold (in mm - default=0). Maps to a command-line argument: `--distthresh1=%.3f`.

> distthresh3a float

>   Discards samples (in matrix3) shorter than this threshold (in mm - default=0). Maps to a command-line argument: `--distthresh3=%.3f`.

> 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: `{}`)

> fibstan integer (int or long)

>   Force a starting fibre for tracking - default=1, i.e. first fibre orientation. Only works if randfib==0. Maps to a command-line argument: `--fibst=%d`.

> fopda pathlike object or string representing an existing file

>   Other mask for binning tract distribution. Maps to a command-line argument: `--fopd=%s`.

> force_dira boolean

>   Use the actual directory name given - i.e. do not add + to make a new directory. Maps to a command-line argument: `--forcedir`. (Nipype default value: `True`)

> inv_xfma pathlike object or string representing a file

>   Transformation matrix taking DTI space to seed space (compulsory when using a warp_field for seeds_to_dti). Maps to a command-line argument: `--invxfm=%s`.

> loop_checka boolean

>   Perform loop_checks on paths - slower, but allows lower curvature threshold. Maps to a command-line argument: `--loopcheck`.

> lrtarget3a pathlike object or string representing an existing file

>   Column-space mask used for Nxn connectivity matrix. Maps to a command-line argument: `--lrtarget3=%s`.

> meshspace‘caret’ or ‘freesurfer’ or ‘first’ or ‘vox’

>   Mesh reference space - either “caret” (default) or “freesurfer” or “first” or “vox”. Maps to a command-line argument: `--meshspace=%s`.

> mod_eulera boolean

>   Use modified euler streamlining. Maps to a command-line argument: `--modeuler`.

> n_samplesan integer (int or long)

>   Number of samples - default=5000. Maps to a command-line argument: `--nsamples=%d`. (Nipype default value: `5000`)

> n_stepsan integer (int or long)

>   Number of steps per sample - default=2000. Maps to a command-line argument: `--nsteps=%d`.

> networka boolean

>   Activate network mode - only keep paths going through at least one seed mask (required if multiple seed masks). Maps to a command-line argument: `--network`.

> omatrix1a boolean

>   Output matrix1 - SeedToSeed Connectivity. Maps to a command-line argument: `--omatrix1`.

> omatrix2a boolean

>   Output matrix2 - SeedToLowResMask. Maps to a command-line argument: `--omatrix2`. Requires inputs: `target2`.

> omatrix3a boolean

>   Output matrix3 (NxN connectivity matrix). Maps to a command-line argument: `--omatrix3`. Requires inputs: `target3`, `lrtarget3`.

> omatrix4a boolean

>   Output matrix4 - DtiMaskToSeed (special Oxford Sparse Format). Maps to a command-line argument: `--omatrix4`.

> onewayconditiona boolean

>   Apply waypoint conditions to each half tract separately. Maps to a command-line argument: `--onewaycondition`.

> opda boolean

>   Outputs path distributions. Maps to a command-line argument: `--opd`. (Nipype default value: `True`)

> os2ta boolean

>   Outputs seeds to targets. Maps to a command-line argument: `--os2t`.

> out_dira pathlike object or string representing an existing directory

>   Directory to put the final volumes in. Maps to a command-line argument: `--dir=%s`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> rand_fib0 or 1 or 2 or 3

>   Options: 0 - default, 1 - to randomly sample initial fibres (with f > fibthresh), 2 - to sample in proportion fibres (with f>fibthresh) to f, 3 - to sample ALL populations at random (even if f<fibthresh). Maps to a command-line argument: `--randfib=%d`.

> random_seeda boolean

>   Random seed. Maps to a command-line argument: `--rseed`.

> s2tastexta boolean

>   Output seed-to-target counts as a text file (useful when seeding from a mesh). Maps to a command-line argument: `--s2tastext`.

> sample_random_pointsa boolean

>   Sample random points within seed voxels. Maps to a command-line argument: `--sampvox`.

> samples_base_namea unicode string

>   The rootname/base_name for samples files. Maps to a command-line argument: `--samples=%s`. (Nipype default value: `merged`)

> seed_refa pathlike object or string representing an existing file

>   Reference vol to define seed space in simple mode - diffusion space assumed if absent. Maps to a command-line argument: `--seedref=%s`.

> simplea boolean

>   Rack from a list of voxels (seed must be a ASCII list of coordinates). Maps to a command-line argument: `--simple`.

> step_lengtha float

>   Step_length in mm - default=0.5. Maps to a command-line argument: `--steplength=%.3f`.

> stop_maska pathlike object or string representing an existing file

>   Stop tracking at locations given by this mask file. Maps to a command-line argument: `--stop=%s`.

> target2a pathlike object or string representing an existing file

>   Low resolution binary brain mask for storing connectivity distribution in matrix2 mode. Maps to a command-line argument: `--target2=%s`.

> target3a pathlike object or string representing an existing file

>   Mask used for NxN connectivity matrix (or Nxn if lrtarget3 is set). Maps to a command-line argument: `--target3=%s`.

> target4a pathlike object or string representing an existing file

>   Brain mask in DTI space. Maps to a command-line argument: `--target4=%s`.

> target_masksa list of items which are a pathlike object or string representing a file

>   List of target masks - required for seeds_to_targets classification. Maps to a command-line argument: `--targetmasks=%s`.

> use_anisotropya boolean

>   Use anisotropy to constrain tracking. Maps to a command-line argument: `--usef`.

> verbose0 or 1 or 2

>   Verbose level, [0-2]. Level 2 is required to output particle files. Maps to a command-line argument: `--verbose=%d`.

> waycond‘OR’ or ‘AND’

>   Waypoint condition. Either “AND” (default) or “OR”. Maps to a command-line argument: `--waycond=%s`.

> wayordera boolean

>   Reject streamlines that do not hit waypoints in given order. Only valid if waycond=AND. Maps to a command-line argument: `--wayorder`.

> waypointsa pathlike object or string representing an existing file

>   Waypoint mask or ascii list of waypoint masks - only keep paths going through ALL the masks. Maps to a command-line argument: `--waypoints=%s`.

> xfma pathlike object or string representing an existing file

>   Transformation matrix taking seed space to DTI space (either FLIRT matrix or FNIRT warp_field) - default is identity. Maps to a command-line argument: `--xfm=%s`.

> fdt_pathsa list of items which are a pathlike object or string representing an existing file

>   Path/name of a 3D image file containing the output connectivity distribution to the seed mask.

> loga pathlike object or string representing an existing file

>   Path/name of a text record of the command that was run.

> lookup_tractspacea pathlike object or string representing an existing file

>   Lookup_tractspace generated by –omatrix2 option.

> matrix1_dota pathlike object or string representing an existing file

>   Output matrix1.dot - SeedToSeed Connectivity.

> matrix2_dota pathlike object or string representing an existing file

>   Output matrix2.dot - SeedToLowResMask.

> matrix3_dota pathlike object or string representing an existing file

>   Output matrix3 - NxN connectivity matrix.

> network_matrixa pathlike object or string representing an existing file

>   The network matrix generated by –omatrix1 option.

> particle_filesa list of items which are a pathlike object or string representing an existing file

>   Files describing all of the tract samples. Generated only if verbose is set to 2.

> targetsa list of items which are a pathlike object or string representing an existing file

>   A list with all generated seeds_to_target files.

> way_totala pathlike object or string representing an existing file

>   Path/name of a text file containing a single number corresponding to the total number of generated tracts that have not been rejected by inclusion/exclusion mask criteria.

## ProjThresh

Link to code

> Bases: FSLCommand

> Wrapped executable: `proj_thresh`.

> Use FSL proj_thresh for thresholding some outputs of probtrack For complete details, see the FDT Documentation <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_thresh.html>

> Example

>     >>> from nipype.interfaces import fsl
>     >>> ldir = ['seeds_to_M1.nii', 'seeds_to_M2.nii']
>     >>> pThresh = fsl.ProjThresh(in_files=ldir, threshold=3)
>     >>> pThresh.cmdline
>     'proj_thresh seeds_to_M1.nii seeds_to_M2.nii 3'

> in_filesa list of items which are a pathlike object or string representing an existing file

>   A list of input volumes. Maps to a command-line argument: `%s` (position: 0).

> thresholdan integer (int or long)

>   Threshold indicating minimum number of seed voxels entering this mask region. Maps to a command-line argument: `%d` (position: 1).

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> 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: `{}`)

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> out_filesa list of items which are a pathlike object or string representing an existing file

>   Path/name of output volume after thresholding.

## TractSkeleton

Link to code

> Bases: FSLCommand

> Wrapped executable: `tbss_skeleton`.

> Use FSL’s tbss_skeleton to skeletonise an FA image or project arbitrary values onto a skeleton.

> There are two ways to use this interface. To create a skeleton from an FA image, just supply the `in_file` and set `skeleton_file` to True (or specify a skeleton filename. To project values onto a skeleton, you must set `project_data` to True, and then also supply values for `threshold`, `distance_map`, and `data_file`. The `search_mask_file` and `use_cingulum_mask` inputs are also used in data projection, but `use_cingulum_mask` is set to True by default. This mask controls where the projection algorithm searches within a circular space around a tract, rather than in a single perpindicular direction.

> Example

>     >>> import nipype.interfaces.fsl as fsl
>     >>> skeletor = fsl.TractSkeleton()
>     >>> skeletor.inputs.in_file = "all_FA.nii.gz"
>     >>> skeletor.inputs.skeleton_file = True
>     >>> skeletor.run()

> in_filea pathlike object or string representing an existing file

>   Input image (typcially mean FA volume). Maps to a command-line argument: `-i %s`.

> alt_data_filea pathlike object or string representing an existing file

>   4D non-FA data to project onto skeleton. Maps to a command-line argument: `-a %s`.

> alt_skeletona pathlike object or string representing an existing file

>   Alternate skeleton to use. Maps to a command-line argument: `-s %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> data_filea pathlike object or string representing an existing file

>   4D data to project onto skeleton (usually FA).

> distance_mapa pathlike object or string representing an existing file

>   Distance map image.

> 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: `{}`)

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> project_dataa boolean

>   Project data onto skeleton. Maps to a command-line argument: `-p %.3f %s %s %s %s`. Requires inputs: `threshold`, `distance_map`, `data_file`.

> projected_dataa pathlike object or string representing a file

>   Input data projected onto skeleton.

> search_mask_filea pathlike object or string representing an existing file

>   Mask in which to use alternate search rule. Mutually exclusive with inputs: `use_cingulum_mask`.

> skeleton_filea boolean or a pathlike object or string representing a file

>   Write out skeleton image. Maps to a command-line argument: `-o %s`.

> thresholda float

>   Skeleton threshold value.

> use_cingulum_maska boolean

>   Perform alternate search using built-in cingulum mask. Mutually exclusive with inputs: `search_mask_file`. (Nipype default value: `True`)

> projected_dataa pathlike object or string representing a file

>   Input data projected onto skeleton.

> skeleton_filea pathlike object or string representing a file

>   Tract skeleton image.

## VecReg

Link to code

> Bases: FSLCommand

> Wrapped executable: `vecreg`.

> Use FSL vecreg for registering vector data For complete details, see the FDT Documentation <http://www.fmrib.ox.ac.uk/fsl/fdt/fdt_vecreg.html>

> Example

>     >>> from nipype.interfaces import fsl
>     >>> vreg = fsl.VecReg(in_file='diffusion.nii',                  affine_mat='trans.mat',                  ref_vol='mni.nii',                  out_file='diffusion_vreg.nii')
>     >>> vreg.cmdline
>     'vecreg -t trans.mat -i diffusion.nii -o diffusion_vreg.nii -r mni.nii'

> in_filea pathlike object or string representing an existing file

>   Filename for input vector or tensor field. Maps to a command-line argument: `-i %s`.

> ref_vola pathlike object or string representing an existing file

>   Filename for reference (target) volume. Maps to a command-line argument: `-r %s`.

> affine_mata pathlike object or string representing an existing file

>   Filename for affine transformation matrix. Maps to a command-line argument: `-t %s`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> 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: `{}`)

> interpolation‘nearestneighbour’ or ‘trilinear’ or ‘sinc’ or ‘spline’

>   Interpolation method : nearestneighbour, trilinear (default), sinc or spline. Maps to a command-line argument: `--interp=%s`.

> maska pathlike object or string representing an existing file

>   Brain mask in input space. Maps to a command-line argument: `-m %s`.

> out_filea pathlike object or string representing a file

>   Filename for output registered vector or tensor field. Maps to a command-line argument: `-o %s`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> ref_maska pathlike object or string representing an existing file

>   Brain mask in output space (useful for speed up of nonlinear reg). Maps to a command-line argument: `--refmask=%s`.

> rotation_mata pathlike object or string representing an existing file

>   Filename for secondary affine matrix if set, this will be used for the rotation of the vector/tensor field. Maps to a command-line argument: `--rotmat=%s`.

> rotation_warpa pathlike object or string representing an existing file

>   Filename for secondary warp field if set, this will be used for the rotation of the vector/tensor field. Maps to a command-line argument: `--rotwarp=%s`.

> warp_fielda pathlike object or string representing an existing file

>   Filename for 4D warp field for nonlinear registration. Maps to a command-line argument: `-w %s`.

> out_filea pathlike object or string representing an existing file

>   Path/name of filename for the registered vector or tensor field.

## XFibres

Link to code

> alias of `nipype.interfaces.fsl.dti.XFibres5`

## XFibres5

Link to code

> Bases: FSLXCommand

> Wrapped executable: `xfibres`.

> Perform model parameters estimation for local (voxelwise) diffusion parameters

> bvalsa pathlike object or string representing an existing file

>   B values file. Maps to a command-line argument: `--bvals=%s`.

> bvecsa pathlike object or string representing an existing file

>   B vectors file. Maps to a command-line argument: `--bvecs=%s`.

> dwia pathlike object or string representing an existing file

>   Diffusion weighted image data file. Maps to a command-line argument: `--data=%s`.

> maska pathlike object or string representing an existing file

>   Brain binary mask file (i.e. from BET). Maps to a command-line argument: `--mask=%s`.

> n_fibresa long integer >= 1

>   Maximum number of fibres to fit in each voxel. Maps to a command-line argument: `--nfibres=%d`. (Nipype default value: `2`)

> all_arda boolean

>   Turn ARD on on all fibres. Maps to a command-line argument: `--allard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> argsa unicode string

>   Additional parameters to the command. Maps to a command-line argument: `%s`.

> burn_ina long integer >= 0

>   Total num of jumps at start of MCMC to be discarded. Maps to a command-line argument: `--burnin=%d`. (Nipype default value: `0`)

> burn_in_no_arda long integer >= 0

>   Num of burnin jumps before the ard is imposed. Maps to a command-line argument: `--burnin_noard=%d`. (Nipype default value: `0`)

> cnlineara boolean

>   Initialise with constrained nonlinear fitting. Maps to a command-line argument: `--cnonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> 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: `{}`)

> f0_arda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0 --ardf0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`, `all_ard`.

> f0_noarda boolean

>   Noise floor model: add to the model an unattenuated signal compartment f0. Maps to a command-line argument: `--f0`. Mutually exclusive with inputs: `f0_noard`, `f0_ard`.

> force_dira boolean

>   Use the actual directory name given (do not add + to make a new directory). Maps to a command-line argument: `--forcedir`. (Nipype default value: `True`)

> fudgean integer (int or long)

>   ARD fudge factor. Maps to a command-line argument: `--fudge=%d`.

> gradnonlina pathlike object or string representing an existing file

>   Gradient file corresponding to slice. Maps to a command-line argument: `--gradnonlin=%s`.

> logdira pathlike object or string representing a directory

>   Maps to a command-line argument: `--logdir=%s`. (Nipype default value: `.`)

> model1 or 2 or 3

>   Use monoexponential (1, default, required for single-shell) or multiexponential (2, multi-shell) model. Maps to a command-line argument: `--model=%d`.

> n_jumpsan integer (int or long)

>   Num of jumps to be made by MCMC. Maps to a command-line argument: `--njumps=%d`. (Nipype default value: `5000`)

> no_arda boolean

>   Turn ARD off on all fibres. Maps to a command-line argument: `--noard`. Mutually exclusive with inputs: `no_ard`, `all_ard`.

> no_spata boolean

>   Initialise with tensor, not spatially. Maps to a command-line argument: `--nospat`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> non_lineara boolean

>   Initialise with nonlinear fitting. Maps to a command-line argument: `--nonlinear`. Mutually exclusive with inputs: `no_spat`, `non_linear`, `cnlinear`.

> output_type‘NIFTI’ or ‘NIFTI_PAIR’ or ‘NIFTI_GZ’ or ‘NIFTI_PAIR_GZ’

>   FSL output type.

> riciana boolean

>   Use Rician noise modeling. Maps to a command-line argument: `--rician`.

> sample_everya long integer >= 0

>   Num of jumps for each sample (MCMC). Maps to a command-line argument: `--sampleevery=%d`. (Nipype default value: `1`)

> seedan integer (int or long)

>   Seed for pseudo random number generator. Maps to a command-line argument: `--seed=%d`.

> update_proposal_everya long integer >= 1

>   Num of jumps for each update to the proposal density std (MCMC). Maps to a command-line argument: `--updateproposalevery=%d`. (Nipype default value: `40`)

> dyadsa list of items which are a pathlike object or string representing an existing file

>   Mean of PDD distribution in vector form.

> fsamplesa list of items which are a pathlike object or string representing an existing file

>   Samples from the distribution on f anisotropy.

> mean_S0samplesa pathlike object or string representing an existing file

>   Mean of distribution on T2wbaseline signal intensity S0.

> mean_dsamplesa pathlike object or string representing an existing file

>   Mean of distribution on diffusivity d.

> mean_fsamplesa list of items which are a pathlike object or string representing an existing file

>   Mean of distribution on f anisotropy.

> mean_tausamplesa pathlike object or string representing an existing file

>   Mean of distribution on tau samples (only with rician noise).

> phsamplesa list of items which are a pathlike object or string representing an existing file

>   Phi samples, per fiber.

> thsamplesa list of items which are a pathlike object or string representing an existing file

>   Theta samples, per fiber.