qsirecon.interfaces.tortoise module

Wrappers for the TORTOISE programs

class qsirecon.interfaces.tortoise.ComputeADMap(**inputs)[source]

Bases: _TensorMapCmdline

Wrapped executable: ComputeADMap.

Mandatory Inputs:

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

Optional Inputs:

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

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

class qsirecon.interfaces.tortoise.ComputeFAMap(**inputs)[source]

Bases: _TensorMapCmdline

Wrapped executable: ComputeFAMap.

Mandatory Inputs:

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

Optional Inputs:

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

  • 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: {})

  • filter_outliers (a boolean) – Maps to a command-line argument: %d (position: 2). (Nipype default value: True)

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

class qsirecon.interfaces.tortoise.ComputeLIMap(**inputs)[source]

Bases: _TensorMapCmdline

Wrapped executable: ComputeLIMap.

Mandatory Inputs:

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

Optional Inputs:

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

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

class qsirecon.interfaces.tortoise.ComputeMAPMRI_NG(**inputs)[source]

Bases: TORTOISEReconCommandLine

Wrapped executable: ComputeMAPMRI_NG.

Mandatory Inputs:

  • in_file (a pathlike object or string representing an existing file) – _mapmri.nii file. Maps to a command-line argument: %s (position: 1).

  • uvec_file (a pathlike object or string representing an existing 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.

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

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

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

class qsirecon.interfaces.tortoise.ComputeMAPMRI_PA(**inputs)[source]

Bases: TORTOISEReconCommandLine

Wrapped executable: ComputeMAPMRI_PA.

Mandatory Inputs:

  • in_file (a pathlike object or string representing an existing file) – _mapmri.nii file. Maps to a command-line argument: %s (position: 1).

  • uvec_file (a pathlike object or string representing an existing 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.

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

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

class qsirecon.interfaces.tortoise.ComputeMAPMRI_RTOP(**inputs)[source]

Bases: TORTOISEReconCommandLine

Wrapped executable: ComputeMAPMRI_RTOP.

Mandatory Inputs:

  • in_file (a pathlike object or string representing an existing file) – _mapmri.nii file. Maps to a command-line argument: %s (position: 1).

  • uvec_file (a pathlike object or string representing an existing 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.

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

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

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

class qsirecon.interfaces.tortoise.ComputeMDMap(from_file=None, resource_monitor=None, **inputs)[source]

Bases: SimpleInterface

Mandatory Inputs:

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

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

Outputs:

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

  • md_metadata (a dictionary with keys which are any value and with values which are any value) – Metadata for the md file.

class qsirecon.interfaces.tortoise.ComputeRDMap(**inputs)[source]

Bases: _TensorMapCmdline

Wrapped executable: ComputeRDMap.

Mandatory Inputs:

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

Optional Inputs:

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

  • 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: {})

  • num_threads (an integer) – Number of OMP threads.

Outputs:

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

class qsirecon.interfaces.tortoise.EstimateMAPMRI(**inputs)[source]

Bases: TORTOISEReconCommandLine

Wrapped executable: EstimateMAPMRI.

Recon Spec Options

big_delta (a float)
Big Delta in seconds.
CLI--big_delta %.7f
map_order (an integer)
MAPMRI order.
CLI--map_order %d
Default4
small_delta (a float)
Small Delta in seconds.
CLI--small_delta %.7f

Developer Information

Mandatory Inputs:

  • bmtxt_file (a pathlike object or string representing an existing file) – Full path to the input bmtxt file.

  • in_file (a pathlike object or string representing a file) – Full path to the input NIFTI DWI. Maps to a command-line argument: --input %s.

Optional Inputs:

  • a0_file (a pathlike object or string representing an existing file) – A0 image computed externally. Maps to a command-line argument: --A0 %s.

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

  • big_delta (a float) – Big Delta in seconds. Maps to a command-line argument: --big_delta %.7f.

  • bval_cutoff (an integer) – Maximum b-value volumes to use for tensor fitting. (Default: use all volumes). Maps to a command-line argument: --bval_cutoff %d.

  • dt_file (a pathlike object or string representing an existing file) – DTI image computed externally. Maps to a command-line argument: --dti %s. Requires inputs: a0_file.

  • 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: {})

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

  • map_order (an integer) – MAPMRI order. Maps to a command-line argument: --map_order %d. (Nipype default value: 4)

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

  • num_threads (an integer) – Number of OMP threads.

  • small_delta (a float) – Small Delta in seconds. Maps to a command-line argument: --small_delta %.7f.

  • voxelwise_bmat_file (a pathlike object or string representing an existing file) – Use voxelwise Bmatrices for gradient non-linearity correction.

Outputs:

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

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

class qsirecon.interfaces.tortoise.EstimateTensor(**inputs)[source]

Bases: TORTOISEReconCommandLine

Wrapped executable: EstimateTensor.

Mandatory Inputs:

  • bmtxt_file (a pathlike object or string representing an existing file) – Full path to the input bmtxt file.

  • in_file (a pathlike object or string representing a file) – Full path to the input NIFTI DWI. Maps to a command-line argument: --input %s.

Optional Inputs:

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

  • bval_cutoff (an integer) – Maximum b-value volumes to use for tensor fitting. (Default: use all volumes). Maps to a command-line argument: --bval_cutoff %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: {})

  • free_water_diffusivity (an integer) – Free water diffusivity in (mu m)^2/s for N2 fitting. Maps to a command-line argument: --free_water_diffusivity %d.

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

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

  • noise_file (a pathlike object or string representing an existing file) – Use this image for weighting and correction of interpolation artifacts.

  • num_threads (an integer) – Number of OMP threads.

  • reg_mode (‘WLLS’ or ‘NLLS’ or ‘RESTORE’ or ‘DIAG’ or ‘N2’ or ‘NT2’) – Regression mode. WLLS: Weighted linear least squares, NLLS: Nonlinear least squares, RESTORE: Robust NLLS, DIAG: Diagonal Only NLLS, N2: Full diffusion tensor + free water NLLS, NT2: One full parenchymal diffusion tensor + one full flow tensor. Maps to a command-line argument: --reg_mode %s. (Nipype default value: WLLS)

  • voxelwise_bmat_file (a pathlike object or string representing an existing file) – Use voxelwise Bmatrices for gradient non-linearity correction.

  • write_cs (a boolean) – Write the Chi-squred image?. Maps to a command-line argument: --write_CS %d. (Nipype default value: True)

Outputs:

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

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

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

class qsirecon.interfaces.tortoise.TORTOISECommandLine(**inputs)[source]

Bases: CommandLine

Support for TORTOISE commands that utilize OpenMP Sets the environment variable ‘OMP_NUM_THREADS’ to the number of threads specified by the input num_threads.

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: {})

  • num_threads (an integer) – Number of OMP threads.

run(**inputs)[source]

Execute this interface.

This interface will not raise an exception if runtime.returncode is non-zero.

Parameters:

  • cwd (specify a folder where the interface should be run)

  • inputs (allows the interface settings to be updated)

Returns:

results – A copy of the instance that was executed, provenance information and, if successful, results

Return type:

nipype.interfaces.base.support.InterfaceResult

class qsirecon.interfaces.tortoise.TORTOISEConvert(from_file=None, resource_monitor=None, **inputs)[source]

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)

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

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

Outputs:

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

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

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

class qsirecon.interfaces.tortoise.TORTOISEReconCommandLine(**inputs)[source]

Bases: TORTOISECommandLine

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: {})

  • num_threads (an integer) – Number of OMP threads.

qsirecon.interfaces.tortoise.make_bmat_file(bvals, bvecs)[source]