nipype.interfaces.mrtrix.tracking module

DiffusionTensorStreamlineTrack

Link to code

Bases: StreamlineTrack

Wrapped executable: streamtrack.

Specialized interface to StreamlineTrack. This interface is used for streamline tracking from diffusion tensor data, and calls the MRtrix function ‘streamtrack’ with the option ‘DT_STREAM’

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> dtstreamtrack = mrt.DiffusionTensorStreamlineTrack()
>>> dtstreamtrack.inputs.in_file = 'data.Bfloat'
>>> dtstreamtrack.inputs.seed_file = 'seed_mask.nii'
>>> dtstreamtrack.run()
Mandatory Inputs:

  • gradient_encoding_file (a pathlike object or string representing an existing file) – Gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2). See FSL2MRTrix. Maps to a command-line argument: -grad %s (position: -2).

  • in_file (a pathlike object or string representing an existing file) – The image containing the source data.The type of data required depends on the type of tracking as set in the preceding argument. For DT methods, the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed. 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.

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

  • desired_number_of_tracks (an integer) – Sets 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(default is 100 for *_STREAM methods, 1000 for *_PROB methods). Maps to a command-line argument: -number %d.

  • do_not_precompute (a boolean) – Turns off precomputation of the legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4. Maps to a command-line argument: -noprecomputed.

  • 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: {})

  • exclude_file (a pathlike object or string representing an existing file) – Exclusion file. Maps to a command-line argument: -exclude %s. Mutually exclusive with inputs: exclude_file, exclude_spec.

  • exclude_spec (a list of from 4 to 4 items which are a float) – Exclusion specification in mm and radius (x y z r). Maps to a command-line argument: -exclude %s (position: 2). Mutually exclusive with inputs: exclude_file, exclude_spec.

  • include_file (a pathlike object or string representing an existing file) – Inclusion file. Maps to a command-line argument: -include %s. Mutually exclusive with inputs: include_file, include_spec.

  • include_spec (a list of from 4 to 4 items which are a float) – Inclusion specification in mm and radius (x y z r). Maps to a command-line argument: -include %s (position: 2). Mutually exclusive with inputs: include_file, include_spec.

  • initial_cutoff_value (a float) – Sets the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff). Maps to a command-line argument: -initcutoff %s.

  • initial_direction (a list of from 2 to 2 items which are an integer) – Specify the initial tracking direction as a vector. Maps to a command-line argument: -initdirection %s.

  • inputmodel (‘DT_STREAM’ or ‘SD_PROB’ or ‘SD_STREAM’) – Input model type. Maps to a command-line argument: %s (position: -3). (Nipype default value: DT_STREAM)

  • mask_file (a pathlike object or string representing an existing file) – Mask file. Only tracks within mask. Maps to a command-line argument: -mask %s. Mutually exclusive with inputs: mask_file, mask_spec.

  • mask_spec (a list of from 4 to 4 items which are a float) – Mask specification in mm and radius (x y z r). Tracks will be terminated when they leave the ROI. Maps to a command-line argument: -mask %s (position: 2). Mutually exclusive with inputs: mask_file, mask_spec.

  • maximum_number_of_tracks (an integer) – Sets 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.

  • maximum_tract_length (a float) – Sets the maximum length of any track in millimeters (default is 200 mm). Maps to a command-line argument: -length %s.

  • minimum_radius_of_curvature (a float) – Set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB). Maps to a command-line argument: -curvature %s.

  • minimum_tract_length (a float) – Sets the minimum length of any track in millimeters (default is 10 mm). Maps to a command-line argument: -minlength %s.

  • no_mask_interpolation (a boolean) – Turns off trilinear interpolation of mask images. Maps to a command-line argument: -nomaskinterp.

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

  • seed_file (a pathlike object or string representing an existing file) – Seed file. Maps to a command-line argument: -seed %s. Mutually exclusive with inputs: seed_file, seed_spec.

  • seed_spec (a list of from 4 to 4 items which are a float) – Seed specification in mm and radius (x y z r). Maps to a command-line argument: -seed %s (position: 2). Mutually exclusive with inputs: seed_file, seed_spec.

  • step_size (a float) – Set the step size of the algorithm in mm (default is 0.2). Maps to a command-line argument: -step %s.

  • stop (a boolean) – Stop track as soon as it enters any of the 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.

Outputs:

tracked (a pathlike object or string representing an existing file) – Output file containing reconstructed tracts.

FilterTracks

Link to code

Bases: CommandLine

Wrapped executable: filter_tracks.

Use regions-of-interest to select a subset of tracks from a given MRtrix track file.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> filt = mrt.FilterTracks()
>>> filt.inputs.in_file = 'tracks.tck'
>>> filt.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Input tracks to be filtered. 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.

  • debug (a boolean) – Display debugging messages. Maps to a command-line argument: -debug (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: {})

  • exclude_file (a pathlike object or string representing an existing file) – Exclusion file. Maps to a command-line argument: -exclude %s. Mutually exclusive with inputs: exclude_file, exclude_spec.

  • exclude_spec (a list of from 4 to 4 items which are a float) – Exclusion specification in mm and radius (x y z r). Maps to a command-line argument: -exclude %s (position: 2). Mutually exclusive with inputs: exclude_file, exclude_spec.

  • include_file (a pathlike object or string representing an existing file) – Inclusion file. Maps to a command-line argument: -include %s. Mutually exclusive with inputs: include_file, include_spec.

  • include_spec (a list of from 4 to 4 items which are a float) – Inclusion specification in mm and radius (x y z r). Maps to a command-line argument: -include %s (position: 2). Mutually exclusive with inputs: include_file, include_spec.

  • invert (a boolean) – Invert the matching process, so that tracks that wouldotherwise have been included are now excluded and vice-versa. Maps to a command-line argument: -invert.

  • minimum_tract_length (a float) – Sets the minimum length of any track in millimeters (default is 10 mm). Maps to a command-line argument: -minlength %s.

  • no_mask_interpolation (a boolean) – Turns off trilinear interpolation of mask images. Maps to a command-line argument: -nomaskinterp.

  • out_file (a pathlike object or string representing a file) – Output filtered track filename. Maps to a command-line argument: %s (position: -1).

  • quiet (a boolean) – Do not display information messages or progress status. Maps to a command-line argument: -quiet (position: 1).

Outputs:

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

ProbabilisticSphericallyDeconvolutedStreamlineTrack

Link to code

Bases: StreamlineTrack

Wrapped executable: streamtrack.

Performs probabilistic tracking using spherically deconvolved data

Specialized interface to StreamlineTrack. This interface is used for probabilistic tracking from spherically deconvolved data, and calls the MRtrix function ‘streamtrack’ with the option ‘SD_PROB’

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> sdprobtrack = mrt.ProbabilisticSphericallyDeconvolutedStreamlineTrack()
>>> sdprobtrack.inputs.in_file = 'data.Bfloat'
>>> sdprobtrack.inputs.seed_file = 'seed_mask.nii'
>>> sdprobtrack.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The image containing the source data.The type of data required depends on the type of tracking as set in the preceding argument. For DT methods, the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed. 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.

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

  • desired_number_of_tracks (an integer) – Sets 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(default is 100 for *_STREAM methods, 1000 for *_PROB methods). Maps to a command-line argument: -number %d.

  • do_not_precompute (a boolean) – Turns off precomputation of the legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4. Maps to a command-line argument: -noprecomputed.

  • 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: {})

  • exclude_file (a pathlike object or string representing an existing file) – Exclusion file. Maps to a command-line argument: -exclude %s. Mutually exclusive with inputs: exclude_file, exclude_spec.

  • exclude_spec (a list of from 4 to 4 items which are a float) – Exclusion specification in mm and radius (x y z r). Maps to a command-line argument: -exclude %s (position: 2). Mutually exclusive with inputs: exclude_file, exclude_spec.

  • include_file (a pathlike object or string representing an existing file) – Inclusion file. Maps to a command-line argument: -include %s. Mutually exclusive with inputs: include_file, include_spec.

  • include_spec (a list of from 4 to 4 items which are a float) – Inclusion specification in mm and radius (x y z r). Maps to a command-line argument: -include %s (position: 2). Mutually exclusive with inputs: include_file, include_spec.

  • initial_cutoff_value (a float) – Sets the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff). Maps to a command-line argument: -initcutoff %s.

  • initial_direction (a list of from 2 to 2 items which are an integer) – Specify the initial tracking direction as a vector. Maps to a command-line argument: -initdirection %s.

  • inputmodel (‘DT_STREAM’ or ‘SD_PROB’ or ‘SD_STREAM’) – Input model type. Maps to a command-line argument: %s (position: -3). (Nipype default value: DT_STREAM)

  • mask_file (a pathlike object or string representing an existing file) – Mask file. Only tracks within mask. Maps to a command-line argument: -mask %s. Mutually exclusive with inputs: mask_file, mask_spec.

  • mask_spec (a list of from 4 to 4 items which are a float) – Mask specification in mm and radius (x y z r). Tracks will be terminated when they leave the ROI. Maps to a command-line argument: -mask %s (position: 2). Mutually exclusive with inputs: mask_file, mask_spec.

  • maximum_number_of_tracks (an integer) – Sets 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.

  • maximum_number_of_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 %s.

  • maximum_tract_length (a float) – Sets the maximum length of any track in millimeters (default is 200 mm). Maps to a command-line argument: -length %s.

  • minimum_radius_of_curvature (a float) – Set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB). Maps to a command-line argument: -curvature %s.

  • minimum_tract_length (a float) – Sets the minimum length of any track in millimeters (default is 10 mm). Maps to a command-line argument: -minlength %s.

  • no_mask_interpolation (a boolean) – Turns off trilinear interpolation of mask images. Maps to a command-line argument: -nomaskinterp.

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

  • seed_file (a pathlike object or string representing an existing file) – Seed file. Maps to a command-line argument: -seed %s. Mutually exclusive with inputs: seed_file, seed_spec.

  • seed_spec (a list of from 4 to 4 items which are a float) – Seed specification in mm and radius (x y z r). Maps to a command-line argument: -seed %s (position: 2). Mutually exclusive with inputs: seed_file, seed_spec.

  • step_size (a float) – Set the step size of the algorithm in mm (default is 0.2). Maps to a command-line argument: -step %s.

  • stop (a boolean) – Stop track as soon as it enters any of the 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.

Outputs:

tracked (a pathlike object or string representing an existing file) – Output file containing reconstructed tracts.

SphericallyDeconvolutedStreamlineTrack

Link to code

Bases: StreamlineTrack

Wrapped executable: streamtrack.

Performs streamline tracking using spherically deconvolved data

Specialized interface to StreamlineTrack. This interface is used for streamline tracking from spherically deconvolved data, and calls the MRtrix function ‘streamtrack’ with the option ‘SD_STREAM’

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> sdtrack = mrt.SphericallyDeconvolutedStreamlineTrack()
>>> sdtrack.inputs.in_file = 'data.Bfloat'
>>> sdtrack.inputs.seed_file = 'seed_mask.nii'
>>> sdtrack.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The image containing the source data.The type of data required depends on the type of tracking as set in the preceding argument. For DT methods, the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed. 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.

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

  • desired_number_of_tracks (an integer) – Sets 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(default is 100 for *_STREAM methods, 1000 for *_PROB methods). Maps to a command-line argument: -number %d.

  • do_not_precompute (a boolean) – Turns off precomputation of the legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4. Maps to a command-line argument: -noprecomputed.

  • 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: {})

  • exclude_file (a pathlike object or string representing an existing file) – Exclusion file. Maps to a command-line argument: -exclude %s. Mutually exclusive with inputs: exclude_file, exclude_spec.

  • exclude_spec (a list of from 4 to 4 items which are a float) – Exclusion specification in mm and radius (x y z r). Maps to a command-line argument: -exclude %s (position: 2). Mutually exclusive with inputs: exclude_file, exclude_spec.

  • include_file (a pathlike object or string representing an existing file) – Inclusion file. Maps to a command-line argument: -include %s. Mutually exclusive with inputs: include_file, include_spec.

  • include_spec (a list of from 4 to 4 items which are a float) – Inclusion specification in mm and radius (x y z r). Maps to a command-line argument: -include %s (position: 2). Mutually exclusive with inputs: include_file, include_spec.

  • initial_cutoff_value (a float) – Sets the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff). Maps to a command-line argument: -initcutoff %s.

  • initial_direction (a list of from 2 to 2 items which are an integer) – Specify the initial tracking direction as a vector. Maps to a command-line argument: -initdirection %s.

  • inputmodel (‘DT_STREAM’ or ‘SD_PROB’ or ‘SD_STREAM’) – Input model type. Maps to a command-line argument: %s (position: -3). (Nipype default value: DT_STREAM)

  • mask_file (a pathlike object or string representing an existing file) – Mask file. Only tracks within mask. Maps to a command-line argument: -mask %s. Mutually exclusive with inputs: mask_file, mask_spec.

  • mask_spec (a list of from 4 to 4 items which are a float) – Mask specification in mm and radius (x y z r). Tracks will be terminated when they leave the ROI. Maps to a command-line argument: -mask %s (position: 2). Mutually exclusive with inputs: mask_file, mask_spec.

  • maximum_number_of_tracks (an integer) – Sets 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.

  • maximum_tract_length (a float) – Sets the maximum length of any track in millimeters (default is 200 mm). Maps to a command-line argument: -length %s.

  • minimum_radius_of_curvature (a float) – Set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB). Maps to a command-line argument: -curvature %s.

  • minimum_tract_length (a float) – Sets the minimum length of any track in millimeters (default is 10 mm). Maps to a command-line argument: -minlength %s.

  • no_mask_interpolation (a boolean) – Turns off trilinear interpolation of mask images. Maps to a command-line argument: -nomaskinterp.

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

  • seed_file (a pathlike object or string representing an existing file) – Seed file. Maps to a command-line argument: -seed %s. Mutually exclusive with inputs: seed_file, seed_spec.

  • seed_spec (a list of from 4 to 4 items which are a float) – Seed specification in mm and radius (x y z r). Maps to a command-line argument: -seed %s (position: 2). Mutually exclusive with inputs: seed_file, seed_spec.

  • step_size (a float) – Set the step size of the algorithm in mm (default is 0.2). Maps to a command-line argument: -step %s.

  • stop (a boolean) – Stop track as soon as it enters any of the 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.

Outputs:

tracked (a pathlike object or string representing an existing file) – Output file containing reconstructed tracts.

StreamlineTrack

Link to code

Bases: CommandLine

Wrapped executable: streamtrack.

Performs tractography using one of the following models: ‘dt_prob’, ‘dt_stream’, ‘sd_prob’, ‘sd_stream’, Where ‘dt’ stands for diffusion tensor, ‘sd’ stands for spherical deconvolution, and ‘prob’ stands for probabilistic.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> streamtrack = mrt.StreamlineTrack()
>>> streamtrack.inputs.inputmodel = 'SD_PROB'
>>> streamtrack.inputs.in_file = 'data.Bfloat'
>>> streamtrack.inputs.seed_file = 'seed_mask.nii'
>>> streamtrack.inputs.mask_file = 'mask.nii'
>>> streamtrack.cmdline
'streamtrack -mask mask.nii -seed seed_mask.nii SD_PROB data.Bfloat data_tracked.tck'
>>> streamtrack.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – The image containing the source data.The type of data required depends on the type of tracking as set in the preceding argument. For DT methods, the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed. 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.

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

  • desired_number_of_tracks (an integer) – Sets 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(default is 100 for *_STREAM methods, 1000 for *_PROB methods). Maps to a command-line argument: -number %d.

  • do_not_precompute (a boolean) – Turns off precomputation of the legendre polynomial values. Warning: this will slow down the algorithm by a factor of approximately 4. Maps to a command-line argument: -noprecomputed.

  • 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: {})

  • exclude_file (a pathlike object or string representing an existing file) – Exclusion file. Maps to a command-line argument: -exclude %s. Mutually exclusive with inputs: exclude_file, exclude_spec.

  • exclude_spec (a list of from 4 to 4 items which are a float) – Exclusion specification in mm and radius (x y z r). Maps to a command-line argument: -exclude %s (position: 2). Mutually exclusive with inputs: exclude_file, exclude_spec.

  • include_file (a pathlike object or string representing an existing file) – Inclusion file. Maps to a command-line argument: -include %s. Mutually exclusive with inputs: include_file, include_spec.

  • include_spec (a list of from 4 to 4 items which are a float) – Inclusion specification in mm and radius (x y z r). Maps to a command-line argument: -include %s (position: 2). Mutually exclusive with inputs: include_file, include_spec.

  • initial_cutoff_value (a float) – Sets the minimum FA or FOD amplitude for initiating tracks (default is twice the normal cutoff). Maps to a command-line argument: -initcutoff %s.

  • initial_direction (a list of from 2 to 2 items which are an integer) – Specify the initial tracking direction as a vector. Maps to a command-line argument: -initdirection %s.

  • inputmodel (‘DT_STREAM’ or ‘SD_PROB’ or ‘SD_STREAM’) – Input model type. Maps to a command-line argument: %s (position: -3). (Nipype default value: DT_STREAM)

  • mask_file (a pathlike object or string representing an existing file) – Mask file. Only tracks within mask. Maps to a command-line argument: -mask %s. Mutually exclusive with inputs: mask_file, mask_spec.

  • mask_spec (a list of from 4 to 4 items which are a float) – Mask specification in mm and radius (x y z r). Tracks will be terminated when they leave the ROI. Maps to a command-line argument: -mask %s (position: 2). Mutually exclusive with inputs: mask_file, mask_spec.

  • maximum_number_of_tracks (an integer) – Sets 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.

  • maximum_tract_length (a float) – Sets the maximum length of any track in millimeters (default is 200 mm). Maps to a command-line argument: -length %s.

  • minimum_radius_of_curvature (a float) – Set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB). Maps to a command-line argument: -curvature %s.

  • minimum_tract_length (a float) – Sets the minimum length of any track in millimeters (default is 10 mm). Maps to a command-line argument: -minlength %s.

  • no_mask_interpolation (a boolean) – Turns off trilinear interpolation of mask images. Maps to a command-line argument: -nomaskinterp.

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

  • seed_file (a pathlike object or string representing an existing file) – Seed file. Maps to a command-line argument: -seed %s. Mutually exclusive with inputs: seed_file, seed_spec.

  • seed_spec (a list of from 4 to 4 items which are a float) – Seed specification in mm and radius (x y z r). Maps to a command-line argument: -seed %s (position: 2). Mutually exclusive with inputs: seed_file, seed_spec.

  • step_size (a float) – Set the step size of the algorithm in mm (default is 0.2). Maps to a command-line argument: -step %s.

  • stop (a boolean) – Stop track as soon as it enters any of the 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.

Outputs:

tracked (a pathlike object or string representing an existing file) – Output file containing reconstructed tracts.

Tracks2Prob

Link to code

Bases: CommandLine

Wrapped executable: tracks2prob.

Convert a tract file into a map of the fraction of tracks to enter each voxel - also known as a tract density image (TDI) - in MRtrix’s image format (.mif). This can be viewed using MRview or converted to Nifti using MRconvert.

Example

>>> import nipype.interfaces.mrtrix as mrt
>>> tdi = mrt.Tracks2Prob()
>>> tdi.inputs.in_file = 'dwi_CSD_tracked.tck'
>>> tdi.inputs.colour = True
>>> tdi.run()
Mandatory Inputs:

in_file (a pathlike object or string representing an existing file) – Tract file. 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.

  • colour (a boolean) – Add colour to the output image according to the direction of the tracks. Maps to a command-line argument: -colour (position: 3).

  • 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: {})

  • fraction (a boolean) – Produce an image of the fraction of fibres through each voxel (as a proportion of the total number in the file), rather than the count. Maps to a command-line argument: -fraction (position: 3).

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

  • output_datatype (‘Bit’ or ‘Int8’ or ‘UInt8’ or ‘Int16’ or ‘UInt16’ or ‘Int32’ or ‘UInt32’ or ‘float32’ or ‘float64’) – “i.e. Bfloat”. Can be “char”, “short”, “int”, “long”, “float” or “double”. Maps to a command-line argument: -datatype %s (position: 2).

  • resample (a float) – Resample the tracks at regular intervals using Hermite interpolation. If omitted, the program will select an appropriate interpolation factor automatically. Maps to a command-line argument: -resample %d (position: 3).

  • template_file (a pathlike object or string representing an existing file) – An image file to be used as a template for the output (the output image will have the same transform and field of view). Maps to a command-line argument: -template %s (position: 1).

  • voxel_dims (a list of from 3 to 3 items which are a float) – Three comma-separated numbers giving the size of each voxel in mm. Maps to a command-line argument: -vox %s (position: 2).

Outputs:

tract_image (a pathlike object or string representing an existing file) – Output tract count or track density image.