caps.diffusion_preproc.fsl_preproc.FslDiffsuionPpreprocessings¶
FslDiffsuionPpreprocessings¶
- class caps.diffusion_preproc.fsl_preproc.FslDiffsuionPpreprocessings(autoexport_nodes_parameters=True, **kwargs)[source]¶
FSL diffusion preprocessings
- Motion Correction (optional)
- Eddy Currents Correction
- Susceptibility Artifacts Correction (optional)
Note
This script rotates the b-vectors to ensure the consistency between the resulting nifti orientation and the b matrix table.
Inputs¶
[Mandatory]
bet_threshold: a float (mandatory)
fractional intensity threshold
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bvals: a file name (mandatory)
the the diffusion b-values
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bvecs: a file name (mandatory)
the diffusion b-vectors
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complex_phase_file: a file name (mandatory)
complex phase input volume
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dw_image: a file name (mandatory)
an existing diffusion weighted image
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generate_binary_mask: a boolean (mandatory)
create binary mask image
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generate_mesh: a boolean (mandatory)
generate a vtk mesh brain surface
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generate_skull: a boolean (mandatory)
create skull image
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magnitude_file: a file name (mandatory)
file containing magnitude image
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phase_file: a file name (mandatory)
raw phase file
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use_4d_input: a boolean (mandatory)
apply to 4D fMRI data
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[Optional]
specified_index_of_ref_image: an integer (optional)
index of the reference b=0 volume
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Outputs¶
affine_transformations: a legal value
path of the calculated rigid transformations
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bet_inskull_mask_file: a file name
path/name of inskull mask (if generated)
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bet_inskull_mesh_file: a file name
path/name of inskull mesh outline (if generated)
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bet_meshfile: a file name
path/name of vtk mesh file (if generated)
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bet_out_file: a file name
path/name of skullstripped file (if generated)
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bet_outskin_mask_file: a file name
path/name of outskin mask (if generated)
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bet_outskin_mesh_file: a file name
path/name of outskin mesh outline (if generated)
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bet_outskull_mask_file: a file name
path/name of outskull mask (if generated)
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bet_outskull_mesh_file: a file name
path/name of outskull mesh outline (if generated)
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bet_skull_mask_file: a file name
path/name of skull mask (if generated)
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corrected_file: any value
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eddy_corrected_files: a file name
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index_of_ref_image: an integer
index of the reference b=0 volume
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motion_corrected_image: a file name
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outelements: a legal value
list of selected values
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reoriented_bvecs: any value
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rigid_transformations: a legal value
path of the calculated rigid transformations
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susceptibility_corrected_file: a file name
unwarped file
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unwrapped_phase_file: a file name
unwrapped phase file
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Pipeline schema¶
