qsirecon.interfaces.mrtrix module

Image tools interfaces

class qsirecon.interfaces.mrtrix.BuildConnectome(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Wrapped executable: tck2connectome.

Generate a connectome matrix from a streamlines file and a node parcellation image.

Example

>>> import nipype.interfaces.mrtrix3 as mrt
>>> mat = mrt.BuildConnectome()
>>> mat.inputs.in_file = "tracks.tck"
>>> mat.inputs.in_parc = "aparc+aseg.nii"
>>> mat.cmdline                               
"tck2connectome tracks.tck aparc+aseg.nii connectome.csv"
>>> mat.run()                                 

Mandatory Inputs:

• in_file (a pathlike object or string representing an existing file) – Input tractography. Maps to a command-line argument: %s (position: -3).

• out_file (a pathlike object or string representing a file) – Output file after processing. Maps to a command-line argument: %s (position: -1). (Nipype default value: connectome.csv)

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• atlas_labels_file (a pathlike object or string representing an existing file) – Parcellation labels file.

• atlas_name (a string) – Name of atlas (for variables in matfile).

• 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: {})

• in_parc (a pathlike object or string representing an existing file) – Parcellation file. Maps to a command-line argument: %s (position: -2).

• in_scalar (a pathlike object or string representing an existing file) – Provide the associated image for the mean_scalar metric. Maps to a command-line argument: -scale_file %s.

• in_weights (a pathlike object or string representing an existing file) – Specify a text scalar file containing the streamline weights. Maps to a command-line argument: -tck_weights_in %s.

• keep_unassigned (a boolean) – By default, the program discards the information regarding those streamlines that are not successfully assigned to a node pair. Set this option to keep these values (will be the first row/column in the output matrix). Maps to a command-line argument: -keep_unassigned.

• length_scale (‘None’ or ‘length’ or ‘invlength’) – Maps to a command-line argument: %s.

• measure (a string) – Name of the connectivity measure.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_assignments (a pathlike object or string representing a file) – File with streamline assignments. Maps to a command-line argument: -out_assignments %s.

• quiet (a boolean) – Maps to a command-line argument: -quiet.

• scale_invnodevol (a boolean) – Maps to a command-line argument: -scale_invnodevol.

• search_forward (a float) – Project the streamline forwards from the endpoint in search of aparcellation node voxel. Argument is the maximum traversal length in mm. Maps to a command-line argument: -assignment_forward_search %f.

• search_radius (a float) – Perform a radial search from each streamline endpoint to locate the nearest node. Argument is the maximum radius in mm; if no node is found within this radius, the streamline endpoint is not assigned to any node. Maps to a command-line argument: -assignment_radial_search %f.

• search_reverse (a float) – Traverse from each streamline endpoint inwards along the streamline, in search of the last node traversed by the streamline. Argument is the maximum traversal length in mm (set to 0 to allow search to continue to the streamline midpoint). Maps to a command-line argument: -assignment_reverse_search %f.

• stat_edge (‘sum’ or ‘mean’ or ‘min’ or ‘max’) – Maps to a command-line argument: -stat_edge %s. (Nipype default value: sum)

• symmetric (a boolean) – Make matrices symmetric on output. Maps to a command-line argument: -symmetric.

• use_sift_weights (a boolean) – (Nipype default value: False)

• vox_lookup (a boolean) – Use a simple voxel lookup value at each streamline endpoint. Maps to a command-line argument: -assignment_voxel_lookup.

• zero_diagonal (a boolean) – Set all diagonal entries in the matrix to zero (these represent streamlines that connect to the same node at both ends). Maps to a command-line argument: -zero_diagonal.

Outputs:

• connectivity_matfile (a pathlike object or string representing an existing file) – The matfile containing connectivity data.

• out_assignments (a pathlike object or string representing an existing file) – Streamline assignment csv.

• out_file (a pathlike object or string representing an existing file) – The output connectivity csv.

class qsirecon.interfaces.mrtrix.CompressConnectome2Tck(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

files (a list of items which are a pathlike object or string representing an existing file)

Optional Inputs:

out_zip (a pathlike object or string representing a file) – (Nipype default value: connectome2tck.zip)

Outputs:

out_zip (a pathlike object or string representing an existing file)

class qsirecon.interfaces.mrtrix.Connectome2Tck(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Wrapped executable: connectome2tck.

Mandatory Inputs:

• in_assignments (a pathlike object or string representing an existing file) – Input tck assignments file. Maps to a command-line argument: %s (position: 1).

• in_tck (a pathlike object or string representing an existing file) – Input tck file. Maps to a command-line argument: %s (position: 0).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• 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: {})

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• in_parc (a pathlike object or string representing an existing file) – Maps to a command-line argument: -exemplars %s.

• input_tck_weights (a pathlike object or string representing an existing file) – Maps to a command-line argument: -tck_weights_in %s.

• keep_self (a boolean) – Maps to a command-line argument: -keep_self.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• out_prefix (a string) – This is a .tck file if ‘-files single’. Maps to a command-line argument: %s (position: 2).

• output_files (‘single’ or ‘per_edge’ or ‘per_node’) – Maps to a command-line argument: -files %s.

• output_tck_weights (a pathlike object or string representing a file) – Maps to a command-line argument: -prefix_tck_weights_out %s. Requires inputs: input_tck_weights.

• quiet (a boolean) – Maps to a command-line argument: -quiet.

Outputs:

• exemplar_tck (a pathlike object or string representing an existing file)

• exemplar_weights (a pathlike object or string representing an existing file)

• out_prefix (any value)

• output_tck_weights (any value)

class qsirecon.interfaces.mrtrix.Dwi2Response(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: ResponseSD

Wrapped executable: dwi2response.

Recon Spec Options

max_sh (a list of items which are an integer)

Maximum harmonic degree of response function - a single value for single-shell response, list for multi-shell response. This can be set with fod['max_sh'] in the reconstruction specification.

CLI-lmax %s

Developer Information

Mandatory Inputs:

• algorithm (‘msmt_5tt’ or ‘dhollander’ or ‘tournier’ or ‘tax’) – Response estimation algorithm (multi-tissue). Maps to a command-line argument: %s (position: 1).

• in_file (a pathlike object or string representing an existing file) – Input DWI image. Maps to a command-line argument: %s (position: -5).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_file (a pathlike object or string representing a file) – Output CSF response text file. Maps to a command-line argument: %s (position: -1).

• 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: {})

• gm_file (a pathlike object or string representing a file) – Output GM response text file. Maps to a command-line argument: %s (position: -2).

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• in_mask (a pathlike object or string representing an existing file) – Provide initial mask image. Maps to a command-line argument: -mask %s.

• max_sh (a list of items which are an integer) – Maximum harmonic degree of response function - a single value for single-shell response, list for multi-shell response. This can be set with fod[‘max_sh’] in the reconstruction specification. Maps to a command-line argument: -lmax %s.

• mtt_file (a pathlike object or string representing a file) – Input 5tt image. Maps to a command-line argument: %s (position: -4).

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• wm_file (a pathlike object or string representing a file) – Output WM response text file. Maps to a command-line argument: %s (position: -3).

Outputs:

• csf_file (a pathlike object or string representing a file) – Output CSF response text file. Maps to a command-line argument: %s.

• gm_file (a pathlike object or string representing a file) – Output GM response text file. Maps to a command-line argument: %s.

• wm_file (a pathlike object or string representing a file) – Output WM response text file. Maps to a command-line argument: %s.

class qsirecon.interfaces.mrtrix.EstimateFOD(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Wrapped executable: dwi2fod.

Estimate fibre orientation distributions from diffusion data using spherical deconvolution

Recon Spec Options

algorithm ('csd' or 'msmt_csd')

FOD algorithm. This can be set with fod['algorithm'] in the reconstruction specification.

CLI%s

Developer Information

Mandatory Inputs:

• algorithm (‘csd’ or ‘msmt_csd’) – FOD algorithm. This can be set with fod[‘algorithm’] in the reconstruction specification. Maps to a command-line argument: %s (position: -8).

• in_file (a pathlike object or string representing an existing file) – Input DWI image. Maps to a command-line argument: %s (position: -7).

• wm_txt (a pathlike object or string representing a file) – WM response text file. Maps to a command-line argument: %s (position: -6).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_odf (a pathlike object or string representing a file) – Output CSF ODF. Maps to a command-line argument: %s (position: -1). Requires inputs: csf_txt.

• csf_txt (a pathlike object or string representing a file) – CSF response text file. Maps to a command-line argument: %s (position: -2).

• 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: {})

• gm_odf (a pathlike object or string representing a file) – Output GM ODF. Maps to a command-line argument: %s (position: -3). Requires inputs: gm_txt.

• gm_txt (a pathlike object or string representing a file) – GM response text file. Maps to a command-line argument: %s (position: -4). Requires inputs: csf_txt.

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• in_dirs (a pathlike object or string representing an existing file) – Specify the directions over which to apply the non-negativity constraint (by default, the built-in 300 direction set is used). These should be supplied as a text file containing the [ az el ] pairs for the directions. Maps to a command-line argument: -directions %s.

• mask_file (a pathlike object or string representing an existing file) – Mask image. Maps to a command-line argument: -mask %s.

• max_sh (a list of items which are an integer) – Maximum harmonic degree of response function - single value for single-shell response, list for multi-shell response. Maps to a command-line argument: -lmax %s.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• shell (a list of items which are a float) – Specify one or more dw gradient shells. Maps to a command-line argument: -shell %s.

• wm_odf (a pathlike object or string representing a file) – Output WM ODF. Maps to a command-line argument: %s (position: -5).

Outputs:

• csf_odf (a pathlike object or string representing a file) – Output CSF ODF.

• csf_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the CSF FOD.

• gm_odf (a pathlike object or string representing a file) – Output GM ODF.

• gm_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the GM FOD.

• wm_odf (a pathlike object or string representing a file) – Output WM ODF.

• wm_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the WM FOD.

class qsirecon.interfaces.mrtrix.GenerateMasked5tt(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: Generate5tt

Wrapped executable: 5ttgen.

Mandatory Inputs:

• algorithm (‘fsl’ or ‘gif’ or ‘freesurfer’ or ‘hsvs’) – Tissue segmentation algorithm. Maps to a command-line argument: %s (position: 0).

• in_file (a pathlike object or string representing an existing file or a string or os.PathLike object referring to an existing directory) – Input T1w image or FreeSurfer directory. Maps to a command-line argument: %s (position: 1).

Optional Inputs:

• amygdala_hipppocampi_subcortical_gm (a boolean) – Maps to a command-line argument: -sgm_amyg_hipp.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• 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: {})

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• hippocampi (‘subfields’ or ‘first’ or ‘aseg’) – Choose the method used to segment the hippocampi. (Only for ‘freesurfer’ algorithm). Maps to a command-line argument: -hippocampi %s.

• hippocampi_method (‘subfields’ or ‘first’ or ‘aseg’) – Maps to a command-line argument: -hippocampi %s.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• lut_file (a pathlike object or string representing an existing file) – Manually provide path to the lookup table on which the input parcellation image is based. (Only for ‘freesurfer’ algorithm). Maps to a command-line argument: -lut %s.

• mask (a pathlike object or string representing an existing file) – Maps to a command-line argument: -mask %s.

• mask_file (a pathlike object or string representing an existing file) – Provide a brain mask image. (Only for ‘fsl’ algorithm). Maps to a command-line argument: -mask %s.

• nocrop (a boolean) – Do not crop the image to the region of interest. Maps to a command-line argument: -nocrop.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• out_file (a pathlike object or string representing a file) – Output image. Maps to a command-line argument: %s (position: 2).

• premasked (a boolean) – Assume that the input image is already brain-masked. (Only for ‘fsl’ algorithm). Maps to a command-line argument: -premasked.

• sgm_amyg_hipp (a boolean) – Include the amygdala and hippocampus in the subcortical grey matter segment. Maps to a command-line argument: -sgm_amyg_hipp.

• t2_image (a pathlike object or string representing an existing file) – Provide a T2-weighted image in addition to the default T1-weighted image. (Only for ‘fsl’ algorithm). Maps to a command-line argument: -t2 %s.

• template (a pathlike object or string representing an existing file) – Provide an image that will form the template for the generated 5TT image. (Only for ‘hsvs’ algorithm). Maps to a command-line argument: -template %s.

• thalami_method (‘nuclei’ or ‘first’ or ‘aseg’) – Maps to a command-line argument: -thalami %s.

• white_stem (a boolean) – Maps to a command-line argument: -white_stem.

Outputs:

out_file (a pathlike object or string representing an existing file) – Output image.

class qsirecon.interfaces.mrtrix.GlobalTractography(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Wrapped executable: tckglobal.

Mandatory Inputs:

• dwi_file (a pathlike object or string representing an existing file) – Full dwi file (source). Maps to a command-line argument: %s (position: -3).

• wm_txt (a pathlike object or string representing an existing file) – Wm response function (response). Maps to a command-line argument: %s (position: -2).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_txt (a pathlike object or string representing an existing file) – Csf isotropic response functions. Maps to a command-line argument: -riso %s.

• 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: {})

• gm_txt (a pathlike object or string representing an existing file) – Gm isotropic response functions. Maps to a command-line argument: -riso %s.

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• mask (a pathlike object or string representing an existing file) – Only reconstruct the tractogram within the specified brain mask image. Maps to a command-line argument: -mask %s.

• niter (an integer) – The number of iterations of the metropolis hastings optimizer. (default = 10M). Maps to a command-line argument: -niter %d.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• out_fod (a pathlike object or string representing a file) – Predicted fibre orientation distribution function (fODF).This fODF is estimated as part of the global track optimization, and therefore incorporates the spatial regularization that it imposes. Internally, the fODF is represented as a discrete sum of apodized point spread functions (aPSF) oriented along the directions of all particles in the voxel, used to predict the DWI signal from the particle configuration. Maps to a command-line argument: -fod %s.

• out_isotropic_fraction (a pathlike object or string representing a file) – Predicted isotropic fractions of the tissues for which response functions were provided with isotropic_response_txt. Typically, these are CSF and GM. Maps to a command-line argument: -fiso %s. Requires inputs: csf_txt.

• out_residual_energy (a pathlike object or string representing a file) – Residual external energy in every voxel. Maps to a command-line argument: -eext %s.

• out_tracks (a pathlike object or string representing a file) – The globally-optimized streamlines (tracks). Maps to a command-line argument: %s (position: -1).

Outputs:

• isotropic_fraction (a pathlike object or string representing an existing file) – Predicted isotropic fractions of the tissues for which response functions were provided with -riso. Typically, these are CSF and GM.

• residual_energy (a pathlike object or string representing an existing file) – Residual external energy in every voxel.

• tck_file (a pathlike object or string representing an existing file) – Global tck file.

• wm_odf (a pathlike object or string representing an existing file) – Predicted fibre orientation distribution function (fODF).This fODF is estimated as part of the global track optimization, and therefore incorporates the spatial regularization that it imposes. Internally, the fODF is represented as a discrete sum of apodized point spread functions (aPSF) oriented along the directions of all particles in the voxel, used to predict the DWI signal from the particle configuration.

class qsirecon.interfaces.mrtrix.ITKTransformConvert(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: transformconvert.

Mandatory Inputs:

in_transform (a string or os.PathLike object referring to an existing file) – Maps to a command-line argument: %s (position: 0).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• 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: {})

• operation (‘itk_import’) – Maps to a command-line argument: %s. (Nipype default value: itk_import)

• out_transform (a string or os.PathLike object) – Maps to a command-line argument: %s (position: -1).

Outputs:

out_transform (a string or os.PathLike object referring to an existing file)

class qsirecon.interfaces.mrtrix.MRTrixAtlasGraph(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Produce one connectivity matrix per atlas based on MRtrix tractography

Mandatory Inputs:

• atlas_configs (a dictionary with keys which are any value and with values which are any value) – Atlas configs for atlases to run connectivity for. Keys are atlas names, values are dictionaries with at least the following keys: ‘labels’ and ‘dwi_resolution_mif’. ‘labels’ is the parcellation labels file, and ‘dwi_resolution_mif’ is the parcellation file in the same resolution as the DWI data, in MIF format.

• in_file (a pathlike object or string representing an existing file) – Input tractography. Maps to a command-line argument: %s (position: -3).

• out_file (a pathlike object or string representing a file) – Output file after processing. Maps to a command-line argument: %s (position: -1). (Nipype default value: connectome.csv)

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• atlas_labels_file (a pathlike object or string representing an existing file) – Parcellation labels file.

• atlas_name (a string) – Name of atlas (for variables in matfile).

• 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: {})

• in_parc (a pathlike object or string representing an existing file) – Parcellation file. Maps to a command-line argument: %s (position: -2).

• in_scalar (a pathlike object or string representing an existing file) – Provide the associated image for the mean_scalar metric. Maps to a command-line argument: -scale_file %s.

• in_weights (a pathlike object or string representing an existing file) – Specify a text scalar file containing the streamline weights. Maps to a command-line argument: -tck_weights_in %s.

• keep_unassigned (a boolean) – By default, the program discards the information regarding those streamlines that are not successfully assigned to a node pair. Set this option to keep these values (will be the first row/column in the output matrix). Maps to a command-line argument: -keep_unassigned.

• length_scale (‘None’ or ‘length’ or ‘invlength’) – Maps to a command-line argument: %s.

• measure (a string) – Name of the connectivity measure.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_assignments (a pathlike object or string representing a file) – File with streamline assignments. Maps to a command-line argument: -out_assignments %s.

• quiet (a boolean) – Maps to a command-line argument: -quiet.

• scale_invnodevol (a boolean) – Maps to a command-line argument: -scale_invnodevol.

• search_forward (a float) – Project the streamline forwards from the endpoint in search of aparcellation node voxel. Argument is the maximum traversal length in mm. Maps to a command-line argument: -assignment_forward_search %f.

• search_radius (a float) – Perform a radial search from each streamline endpoint to locate the nearest node. Argument is the maximum radius in mm; if no node is found within this radius, the streamline endpoint is not assigned to any node. Maps to a command-line argument: -assignment_radial_search %f.

• search_reverse (a float) – Traverse from each streamline endpoint inwards along the streamline, in search of the last node traversed by the streamline. Argument is the maximum traversal length in mm (set to 0 to allow search to continue to the streamline midpoint). Maps to a command-line argument: -assignment_reverse_search %f.

• stat_edge (‘sum’ or ‘mean’ or ‘min’ or ‘max’) – Maps to a command-line argument: -stat_edge %s. (Nipype default value: sum)

• symmetric (a boolean) – Make matrices symmetric on output. Maps to a command-line argument: -symmetric.

• tracking_params (a list of items which are any value) – List of sets of parameters for tck2connectome.

• use_sift_weights (a boolean) – (Nipype default value: False)

• vox_lookup (a boolean) – Use a simple voxel lookup value at each streamline endpoint. Maps to a command-line argument: -assignment_voxel_lookup.

• zero_diagonal (a boolean) – Set all diagonal entries in the matrix to zero (these represent streamlines that connect to the same node at both ends). Maps to a command-line argument: -zero_diagonal.

Outputs:

• commands (a pathlike object or string representing a file)

• connectivity_matfile (a pathlike object or string representing an existing file)

• exemplar_files (a list of items which are a pathlike object or string representing an existing file)

class qsirecon.interfaces.mrtrix.MRTrixGradientTable(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

• bval_file (a pathlike object or string representing an existing file)

• bvec_file (a pathlike object or string representing an existing file)

Outputs:

gradient_file (a pathlike object or string representing an existing file)

class qsirecon.interfaces.mrtrix.MRTrixIngress(from_file=None, resource_monitor=None, **inputs)

Bases: SimpleInterface

Mandatory Inputs:

dwi_file (a pathlike object or string representing an existing file)

Optional Inputs:

• b_file (a pathlike object or string representing an existing file)

• bval_file (a pathlike object or string representing an existing file)

• bvec_file (a pathlike object or string representing an existing file)

• suffix (a string) – (Nipype default value: "")

Outputs:

mif_file (a pathlike object or string representing a file)

class qsirecon.interfaces.mrtrix.MTNormalize(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: SS3TBase

Wrapped executable: mtnormalise.

Mandatory Inputs:

• mask_file (a pathlike object or string representing an existing file) – Mask image. Maps to a command-line argument: -mask %s.

• wm_odf (a pathlike object or string representing a file) – WM ODF image. Maps to a command-line argument: %s (position: 0).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_normed_odf (a pathlike object or string representing a file) – Output CSF normed_odf. Maps to a command-line argument: %s (position: 5).

• csf_odf (a pathlike object or string representing a file) – CSF ODF image. Maps to a command-line argument: %s (position: 4).

• 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: {})

• gm_normed_odf (a pathlike object or string representing a file) – Output GM normed_odf. Maps to a command-line argument: %s (position: 3).

• gm_odf (a pathlike object or string representing a file) – GM ODF image. Maps to a command-line argument: %s (position: 2).

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• inlier_mask (a pathlike object or string representing a file) – Estimated spatially varying intensity level that is used for normalisation. Maps to a command-line argument: -check_mask %s.

• norm_image (a pathlike object or string representing a file) – Final mask used to compute the normalisation. This mask excludes regions identified as outliers by the optimisation process. Maps to a command-line argument: -check_norm %s.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• wm_normed_odf (a pathlike object or string representing a file) – Output WM normed_odf. Maps to a command-line argument: %s (position: 1).

Outputs:

• csf_normed_odf (a pathlike object or string representing a file) – Normalized CSF ODF.

• gm_normed_odf (a pathlike object or string representing a file) – Normalized GM ODF.

• inlier_mask (a pathlike object or string representing a file) – Final mask used to compute the normalisation. This mask excludes regions identified as outliers by the optimisation process.

• norm_image (a pathlike object or string representing a file) – Estimated spatially varying intensity level that is used for normalisation.

• wm_normed_odf (a pathlike object or string representing a file) – Normalized WM ODF.

class qsirecon.interfaces.mrtrix.SIFT2(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Wrapped executable: tcksift2.

Mandatory Inputs:

• in_fod (a pathlike object or string representing an existing file) – Input FOD SH file. Maps to a command-line argument: %s (position: -2).

• in_tracks (a pathlike object or string representing an existing file) – Input tck file. Maps to a command-line argument: %s (position: -3).

Optional Inputs:

• act_file (a pathlike object or string representing an existing file) – Use the Anatomically-Constrained Tractography framework during tracking; provided image must be in the 5TT (five - tissue - type) format. Maps to a command-line argument: -act %s.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• 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: {})

• fd_scale_gm (a boolean) – Provide this option (in conjunction with -act) to heuristically downsize the fibre density estimates based on the presence of GM in the voxel. This can assist in reducing tissue interface effects when using a single-tissue deconvolution algorithm. Maps to a command-line argument: -fd_scale_gm. Requires inputs: act_file.

• fd_thresh (a float) – Fibre density threshold; exclude an FOD lobe from filtering processing if its integral is less than this amount (streamlines will still be mapped to it, but it will not contribute to the cost function or the filtering). Maps to a command-line argument: -fd_thresh %f.

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• make_null_lobes (a boolean) – Add an additional FOD lobe to each voxel, with zero integral, that covers all directions with zero / negative FOD amplitudes. Maps to a command-line argument: -make_null_lobes.

• no_dilate_lut (a boolean) – Do NOT dilate FOD lobe lookup tables; only map streamlines to FOD lobes if the precise tangent lies within the angular spread of that lobe. Maps to a command-line argument: -no_dilate_lut.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• out_mu (a string or os.PathLike object) – Output the final value of SIFT proportionality coefficient mu to a text file. Maps to a command-line argument: -out_mu %s.

• out_weights (a pathlike object or string representing a file) – Output text file containing the weightingfactor for each streamline. Maps to a command-line argument: %s (position: -1).

• remove_untracked (a boolean) – Remove FOD lobes that do not have any streamline density attributed to them; this improves filtering slightly, at the expense of longer computation time (and you can no longer do quantitative comparisons between reconstructions if this is enabled). Maps to a command-line argument: -remove_untracked.

Outputs:

• out_mu (a pathlike object or string representing an existing file)

• out_weights (a pathlike object or string representing an existing file)

class qsirecon.interfaces.mrtrix.SS3TBase(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: MRTrix3Base

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• 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: {})

class qsirecon.interfaces.mrtrix.SS3TDwi2Response(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: SS3TBase, Dwi2Response

Wrapped executable: dwi2response.

Recon Spec Options

max_sh (a list of items which are an integer)

Maximum harmonic degree of response function - a single value for single-shell response, list for multi-shell response. This can be set with fod['max_sh'] in the reconstruction specification.

CLI-lmax %s

Developer Information

Mandatory Inputs:

• algorithm (‘msmt_5tt’ or ‘dhollander’ or ‘tournier’ or ‘tax’) – Response estimation algorithm (multi-tissue). Maps to a command-line argument: %s (position: 1).

• in_file (a pathlike object or string representing an existing file) – Input DWI image. Maps to a command-line argument: %s (position: -5).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_file (a pathlike object or string representing a file) – Output CSF response text file. Maps to a command-line argument: %s (position: -1).

• 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: {})

• gm_file (a pathlike object or string representing a file) – Output GM response text file. Maps to a command-line argument: %s (position: -2).

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• in_mask (a pathlike object or string representing an existing file) – Provide initial mask image. Maps to a command-line argument: -mask %s.

• max_sh (a list of items which are an integer) – Maximum harmonic degree of response function - a single value for single-shell response, list for multi-shell response. This can be set with fod[‘max_sh’] in the reconstruction specification. Maps to a command-line argument: -lmax %s.

• mtt_file (a pathlike object or string representing a file) – Input 5tt image. Maps to a command-line argument: %s (position: -4).

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• wm_file (a pathlike object or string representing a file) – Output WM response text file. Maps to a command-line argument: %s (position: -3).

Outputs:

• csf_file (a pathlike object or string representing a file) – Output CSF response text file. Maps to a command-line argument: %s.

• gm_file (a pathlike object or string representing a file) – Output GM response text file. Maps to a command-line argument: %s.

• wm_file (a pathlike object or string representing a file) – Output WM response text file. Maps to a command-line argument: %s.

class qsirecon.interfaces.mrtrix.SS3TEstimateFOD(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: SS3TBase, EstimateFOD

Wrapped executable: /opt/3Tissue/bin/ss3t_csd_beta1.

Mandatory Inputs:

• in_file (a pathlike object or string representing an existing file) – Input DWI image. Maps to a command-line argument: %s (position: -7).

• wm_txt (a pathlike object or string representing a file) – WM response text file. Maps to a command-line argument: %s (position: -6).

Optional Inputs:

• algorithm (a string) – Not needed for ss3t.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• csf_odf (a pathlike object or string representing a file) – Output CSF ODF. Maps to a command-line argument: %s (position: -1). Requires inputs: csf_txt.

• csf_txt (a pathlike object or string representing a file) – CSF response text file. Maps to a command-line argument: %s (position: -2).

• 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: {})

• gm_odf (a pathlike object or string representing a file) – Output GM ODF. Maps to a command-line argument: %s (position: -3). Requires inputs: gm_txt.

• gm_txt (a pathlike object or string representing a file) – GM response text file. Maps to a command-line argument: %s (position: -4). Requires inputs: csf_txt.

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• in_dirs (a pathlike object or string representing an existing file) – Specify the directions over which to apply the non-negativity constraint (by default, the built-in 300 direction set is used). These should be supplied as a text file containing the [ az el ] pairs for the directions. Maps to a command-line argument: -directions %s.

• mask_file (a pathlike object or string representing an existing file) – Mask image. Maps to a command-line argument: -mask %s.

• max_sh (a list of items which are an integer) – Maximum harmonic degree of response function - single value for single-shell response, list for multi-shell response. Maps to a command-line argument: -lmax %s.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• shell (a list of items which are a float) – Specify one or more dw gradient shells. Maps to a command-line argument: -shell %s.

• wm_odf (a pathlike object or string representing a file) – Output WM ODF. Maps to a command-line argument: %s (position: -5).

Outputs:

• csf_odf (a pathlike object or string representing a file) – Output CSF ODF.

• csf_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the CSF FOD.

• gm_odf (a pathlike object or string representing a file) – Output GM ODF.

• gm_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the GM FOD.

• wm_odf (a pathlike object or string representing a file) – Output WM ODF.

• wm_odf_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the WM FOD.

class qsirecon.interfaces.mrtrix.TckGen(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: Tractography

Wrapped executable: tckgen.

Mandatory Inputs:

• in_file (a pathlike object or string representing an existing file) – Input file to be processed. Maps to a command-line argument: %s (position: -2).

• out_file (a pathlike object or string representing a file) – Output file containing tracks. Maps to a command-line argument: %s (position: -1). (Nipype default value: tracked.tck)

Optional Inputs:

• act_file (a pathlike object or string representing an existing file) – Use the Anatomically-Constrained Tractography framework during tracking; provided image must be in the 5TT (five - tissue - type) format. Maps to a command-line argument: -act %s.

• algorithm (‘iFOD2’ or ‘FACT’ or ‘iFOD1’ or ‘Nulldist’ or ‘SD_Stream’ or ‘Tensor_Det’ or ‘Tensor_Prob’) – Tractography algorithm to be used – References:[FACT], [iFOD1], [iFOD2], [Nulldist], [Tensor_Det], [Tensor_Prob]. Maps to a command-line argument: -algorithm %s. (Nipype default value: iFOD2)

• angle (a float) – Set the maximum angle between successive steps (default is 90deg x stepsize / voxelsize). Maps to a command-line argument: -angle %f.

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• backtrack (a boolean) – Allow tracks to be truncated. Maps to a command-line argument: -backtrack.

• bval_scale (‘yes’ or ‘no’) – Specifies whether the b - values should be scaled by the square of the corresponding DW gradient norm, as often required for multishell or DSI DW acquisition schemes. The default action can also be set in the MRtrix config file, under the BValueScaling entry. Valid choices are yes / no, true / false, 0 / 1 (default: true). Maps to a command-line argument: -bvalue_scaling %s.

• crop_at_gmwmi (a boolean) – Crop streamline endpoints more precisely as they cross the GM-WM interface. Maps to a command-line argument: -crop_at_gmwmi.

• cutoff (a float) – Set the FA or FOD amplitude cutoff for terminating tracks (default is 0.1). Maps to a command-line argument: -cutoff %f.

• cutoff_init (a float) – Set the minimum FA or FOD amplitude for initiating tracks (default is the same as the normal cutoff). Maps to a command-line argument: -initcutoff %f.

• downsample (an integer) – Maps to a command-line argument: -downsample %d.

• 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: {})

• grad_file (a pathlike object or string representing an existing file) – Dw gradient scheme (MRTrix format). Maps to a command-line argument: -grad %s. Mutually exclusive with inputs: grad_fsl.

• grad_fsl (a tuple of the form: (a pathlike object or string representing an existing file, a pathlike object or string representing an existing file)) – (bvecs, bvals) dw gradient scheme (FSL format). Maps to a command-line argument: -fslgrad %s %s. Mutually exclusive with inputs: grad_file.

• in_bval (a pathlike object or string representing an existing file) – Bvals file in FSL format.

• in_bvec (a pathlike object or string representing an existing file) – Bvecs file in FSL format. Maps to a command-line argument: -fslgrad %s %s.

• init_dir (a tuple of the form: (a float, a float, a float)) – Specify an initial direction for the tracking (this should be supplied as a vector of 3 comma-separated values. Maps to a command-line argument: -initdirection %f,%f,%f.

• max_length (a float) – Set the maximum length of any track in mm (default is 100 x voxelsize). Maps to a command-line argument: -maxlength %f.

• max_seed_attempts (an integer) – Set the maximum number of times that the tracking algorithm should attempt to find an appropriate tracking direction from a given seed point. Maps to a command-line argument: -max_seed_attempts %d.

• max_tracks (an integer) – Set the maximum number of tracks to generate. The program will not generate more tracks than this number, even if the desired number of tracks hasn’t yet been reached (default is 100 x number). Maps to a command-line argument: -maxnum %d.

• min_length (a float) – Set the minimum length of any track in mm (default is 5 x voxelsize). Maps to a command-line argument: -minlength %f.

• n_samples (an integer) – Set the number of FOD samples to take per step for the 2nd order (iFOD2) method. Maps to a command-line argument: -samples %d. (Nipype default value: 4)

• n_tracks (an integer) – NOT supported, do not use.

• n_trials (an integer) – Set the maximum number of sampling trials at each point (only used for probabilistic tracking). Maps to a command-line argument: -trials %d.

• noprecompt (a boolean) – Do NOT pre-compute legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4. Maps to a command-line argument: -noprecomputed.

• nthreads (an integer) – Number of threads. if zero, the number of available cpus will be used. Maps to a command-line argument: -nthreads %d.

• out_bval (a pathlike object or string representing a file) – Export bval file in FSL format.

• out_bvec (a pathlike object or string representing a file) – Export bvec file in FSL format. Maps to a command-line argument: -export_grad_fsl %s %s.

• out_seeds (a pathlike object or string representing a file) – Output the seed location of all successful streamlines to a file. Maps to a command-line argument: -output_seeds %s. (Nipype default value: out_seeds.nii.gz)

• power (a float) – Maps to a command-line argument: -power %f.

• quiet (a boolean) – Maps to a command-line argument: -quiet.

• roi_excl (a pathlike object or string representing an existing file or a tuple of the form: (a float, a float, a float, a float)) – Specify an exclusion region of interest, streamlines that enter ANY exclude region will be discarded. Maps to a command-line argument: -exclude %s.

• roi_incl (a pathlike object or string representing an existing file or a tuple of the form: (a float, a float, a float, a float)) – Specify an inclusion region of interest, streamlines must traverse ALL inclusion regions to be accepted. Maps to a command-line argument: -include %s.

• roi_mask (a pathlike object or string representing an existing file or a tuple of the form: (a float, a float, a float, a float)) – Specify a masking region of interest. If defined,streamlines exiting the mask will be truncated. Maps to a command-line argument: -mask %s.

• seed_dynamic (a pathlike object or string representing an existing file) – Determine seed points dynamically using the SIFT model (must not provide any other seeding mechanism). Note that while this seeding mechanism improves the distribution of reconstructed streamlines density, it should NOT be used as a substitute for the SIFT method itself. Maps to a command-line argument: -seed_dynamic %s.

• seed_gmwmi (a pathlike object or string representing an existing file) – Seed from the grey matter - white matter interface (only valid if using ACT framework). Maps to a command-line argument: -seed_gmwmi %s. Requires inputs: act_file.

• seed_grid_voxel (a tuple of the form: (a pathlike object or string representing an existing file, an integer)) – Seed a fixed number of streamlines per voxel in a mask image; place seeds on a 3D mesh grid (grid_size argument is per axis; so a grid_size of 3 results in 27 seeds per voxel). Maps to a command-line argument: -seed_grid_per_voxel %s %d. Mutually exclusive with inputs: seed_image, seed_rnd_voxel.

• seed_image (a pathlike object or string representing an existing file) – Seed streamlines entirely at random within mask. Maps to a command-line argument: -seed_image %s.

• seed_rejection (a pathlike object or string representing an existing file) – Seed from an image using rejection sampling (higher values = more probable to seed from. Maps to a command-line argument: -seed_rejection %s.

• seed_rnd_voxel (a tuple of the form: (a pathlike object or string representing an existing file, an integer)) – Seed a fixed number of streamlines per voxel in a mask image; random placement of seeds in each voxel. Maps to a command-line argument: -seed_random_per_voxel %s %d. Mutually exclusive with inputs: seed_image, seed_grid_voxel.

• seed_sphere (a tuple of the form: (a float, a float, a float, a float)) – Spherical seed. Maps to a command-line argument: -seed_sphere %f,%f,%f,%f.

• select (an integer) – Set the desired number of tracks. The program will continue to generate tracks until this number of tracks have been selected and written to the output file. Maps to a command-line argument: -select %d.

• sph_trait (a tuple of the form: (a float, a float, a float, a float)) – Maps to a command-line argument: %f,%f,%f,%f.

• step_size (a float) – Set the step size of the algorithm in mm (default is 0.1 x voxelsize; for iFOD2: 0.5 x voxelsize). Maps to a command-line argument: -step %f.

• stop (a boolean) – Stop propagating a streamline once it has traversed all include regions. Maps to a command-line argument: -stop.

• unidirectional (a boolean) – Track from the seed point in one direction only (default is to track in both directions). Maps to a command-line argument: -unidirectional.

• use_rk4 (a boolean) – Use 4th-order Runge-Kutta integration (slower, but eliminates curvature overshoot in 1st-order deterministic methods). Maps to a command-line argument: -rk4.

Outputs:

• out_file (a pathlike object or string representing an existing file) – The output filtered tracks.

• out_seeds (a pathlike object or string representing a file) – Output the seed location of all successful streamlines to a file.

class qsirecon.interfaces.mrtrix.TransformHeader(command=None, terminal_output=None, write_cmdline=False, **inputs)

Bases: CommandLine

Wrapped executable: mrtransform -strides -1,-2,3.

Mandatory Inputs:

• in_image (a string or os.PathLike object referring to an existing file) – Maps to a command-line argument: %s (position: 1).

• transform_file (a string or os.PathLike object referring to an existing file) – Maps to a command-line argument: -linear %s (position: 0).

Optional Inputs:

• args (a string) – Additional parameters to the command. Maps to a command-line argument: %s.

• 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: {})

• out_image (a string or os.PathLike object) – Maps to a command-line argument: %s (position: -1).

Outputs:

out_image (a pathlike object or string representing an existing file)

qsirecon.interfaces.mrtrix.response_function_to_bids(response_function_file)

Load a response function from MRtrix3 and convert to JSON-compatible format.