qsirecon.interfaces.tortoise module

Wrappers for the TORTOISE programs

class qsirecon.interfaces.tortoise.ComputeADMap(**inputs)

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)

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)

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)

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)

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)

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.ComputeRDMap(**inputs)

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.DRBUDDI(**inputs)

Bases: TORTOISECommandLine

Wrapped executable: DRBUDDI.

Mandatory Inputs:

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

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

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

• fieldmap_type (‘epi’ or ‘rpe_series’)

Optional Inputs:

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

• blip_assignments (a list of items which are any value)

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

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

• disable_initial_rigid (a boolean) – DRBUDDI performs an initial registration between the up and down data.This registration starts with rigid, followed by a quick diffeomorphic and finalized by another rigid. This parameter, when set to 1 disables all these registrations. Default: False. Maps to a command-line argument: --DRBUDDI_disable_initial_rigid %d.

• disable_itk_threads (a boolean) – Maps to a command-line argument: --disable_itk_threads. (Nipype default value: True)

• 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: {})

• estimate_learning_rate_per_iteration (a boolean) – Flat to estimate learning rate at every iteration. Makes DRBUDDI slower but better results. Default: False. Maps to a command-line argument: --DRBUDDI_estimate_LR_per_iteration %d.

• num_threads (an integer) – Number of OMP threads. Maps to a command-line argument: --ncores %d.

• sloppy (a boolean) – Use underpowered (sloppy) registration for speed. Maps to a command-line argument: --DRBUDDI_stage [learning_rate={0.3},cfs={100:8:4},field_smoothing={9:0},metrics={MSJac:CC},restrict_constrain={1:1}].

• start_with_diffeomorphic_for_rigid_reg (a boolean) – DRBUDDI performs an initial registration between the up and down data. This registration starts with rigid, followed by a quick diffeomorphic and finalized by another rigid. This parameter, when set to 1 disables the very initial rigid registration and starts with the quick diffemorphic. This is helpful with VERY DISTORTED data, for which the initial rigid registration is problematic. Default: False. Maps to a command-line argument: --DRBUDDI_start_with_diffeomorphic_for_rigid_reg.

• structural_image (a list of items which are a pathlike object or string representing an existing file) – Maps to a command-line argument: -s %s.

• tensor_fit_bval_max (an integer) – Up to which b-value should be used for DRBUDDI’s tensor fitting. Default: 0 , meaning use all b-values. Maps to a command-line argument: --DRBUDDI_DWI_bval_tensor_fitting %d.

Outputs:

• bdown_to_bup_rigid_trans_h5 (a pathlike object or string representing an existing file)

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

• blip_down_b0 (a pathlike object or string representing an existing file)

• blip_down_b0_corrected (a pathlike object or string representing an existing file)

• blip_down_b0_corrected_jac (a pathlike object or string representing an existing file)

• blip_down_b0_quad (a pathlike object or string representing an existing file)

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

• blip_up_b0 (a pathlike object or string representing an existing file)

• blip_up_b0_corrected (a pathlike object or string representing an existing file)

• blip_up_b0_corrected_jac (a pathlike object or string representing an existing file)

• blip_up_b0_quad (a pathlike object or string representing an existing file)

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

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

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

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

class qsirecon.interfaces.tortoise.EstimateMAPMRI(**inputs)

Bases: TORTOISEReconCommandLine

Wrapped executable: EstimateMAPMRI.

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)

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 weigthing 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)

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)

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)

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)

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)