qsiprep.interfaces.tortoise module
Wrappers for the TORTOISE programs
- class qsiprep.interfaces.tortoise.DRBUDDI(**inputs)[source]
Bases:
TORTOISECommandLineWrapped 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={0.4},cfs={4:2:1},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 qsiprep.interfaces.tortoise.DRBUDDIAggregateOutputs(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface- Mandatory Inputs:
fieldmap_type (‘epi’ or ‘rpe_series’)
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.bdown_to_bup_rigid_trans_h5 (a pathlike object or string representing an existing file)
blip_assignments (a list of items which are any value)
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) – Blip up to b0_corrected.
deformation_minv (a pathlike object or string representing an existing 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:
{})num_threads (an integer) – Number of OMP threads.
structural_image (a pathlike object or string representing an existing file)
undistorted_reference (a pathlike object or string representing an existing file)
wm_seg (a pathlike object or string representing an existing file) – White matter segmentation image.
- Outputs:
b0_ref (a pathlike object or string representing an existing file)
down_fa_corrected_image (a pathlike object or string representing an existing file)
sdc_scaling_images (a list of items which are a pathlike object or string representing an existing file)
sdc_warps (a list of items which are a pathlike object or string representing an existing file)
up_fa_corrected_image (a pathlike object or string representing an existing file)
- class qsiprep.interfaces.tortoise.GatherDRBUDDIInputs(from_file=None, resource_monitor=None, **inputs)[source]
Bases:
SimpleInterface- Mandatory Inputs:
dwi_series_pedir (‘i’ or ‘i-’ or ‘j’ or ‘j-’ or ‘k’ or ‘k-’)
fieldmap_type (‘epi’ or ‘rpe_series’)
- Optional Inputs:
args (a string) – Additional parameters to the command. Maps to a command-line argument:
%s.b0_threshold (an integer) – (Nipype default value:
100)bval_files (a list of items which are a pathlike object or string representing an existing file or a pathlike object or string representing an existing file)
bvec_files (a list of items which are a pathlike object or string representing an existing file or a pathlike object or string representing an existing file)
dwi_files (a list of items which are a pathlike object or string representing an existing 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:
{})epi_fmaps (a list of items which are a pathlike object or string representing an existing file) – Files from fmaps/ for distortion correction.
num_threads (an integer) – Number of OMP threads.
original_files (a list of items which are a pathlike object or string representing an existing file)
raw_image_sdc (a boolean) – (Nipype default value:
True)
- Outputs:
blip_assignments (a list of items which are any value)
blip_down_bmat (a pathlike object or string representing an existing file)
blip_down_image (a pathlike object or string representing an existing file)
blip_up_bmat (a pathlike object or string representing an existing file)
blip_up_image (a pathlike object or string representing an existing file)
blip_up_json (a pathlike object or string representing an existing file)
report (a string)
- class qsiprep.interfaces.tortoise.Gibbs(**kwargs)[source]
Bases:
SeriesPreprocReport,TORTOISECommandLineWrapped executable:
Gibbs.- Mandatory Inputs:
in_file (a string or os.PathLike object referring to an existing file) – Maps to a command-line argument:
%s(position: 0).kspace_coverage (a float) – Maps to a command-line argument:
%.4f(position: 2).phase_encoding_dir (0 or 1) – 0: horizontal, 1:vertical. Maps to a command-line argument:
%d(position: 3).
- 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:
{})mask (a pathlike object or string representing a file)
min_w (an integer)
nmse_text (a string or os.PathLike object)
nsh (an integer) – Maps to a command-line argument:
%d(position: 4).num_threads (an integer) – (Nipype default value:
1)out_file (a string or os.PathLike object) – Maps to a command-line argument:
%s(position: 1).out_report (a pathlike object or string representing a file) – Filename for the visual report. (Nipype default value:
report)
- Outputs:
nmse_text (a string or os.PathLike object) – Nmse between input and output volumes.
out_file (a pathlike object or string representing an existing file)
out_report (a pathlike object or string representing a file) – Filename for the visual report.
- class qsiprep.interfaces.tortoise.TORTOISECommandLine(**inputs)[source]
Bases:
CommandLineSupport 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:
- class qsiprep.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)
- qsiprep.interfaces.tortoise.generate_drbuddi_boilerplate(fieldmap_type, t2w_sdc, with_topup=False)[source]
Generate boilerplate that describes how DRBUDDI is being used.