TensorMetrics brick¶
Compute metrics from tensors¶
Generate maps of tensor-derived parameters as the mean apparent diffusion coefficient (ADC), the fractional anisotropy (FA), the axial diffusivity (AD), the radial diffusivity (RD), the linearity metric, the planarity metric, the sphericity metric, the selected eigenvalue(s) of the diffusion tensor or the selected eigenvector(s) of the diffusion tensor.
(mrtrix tensor2metric command)
Please note that, in mia_processes, MRtrix bricks required diffusion data in MRtrix .mif format. The MRConvert brick could be used to convert diffusion data in NIfTI format into MRtrix .mif format. In this case, bvec and bval file should be specified.
Mandatory inputs parameters:
- in_file (a pathlike object or a string representing an existing file)
Input tensor image (valid extensions: [.mif]).
ex. '/home/username/data/derived_data/DWI_dti.mif'
Optional inputs with default value parameters:
- modulate (FA or none or eigval, default value is FA, optional)
Specify how to modulate the magnitude of the eigenvectors.
ex. FA
- get_ad (a boolean, default value is False, optional)
Compute the axial diffusivity (AD) of the diffusion tensor.
ex. False
- get_adc (a boolean, default value is True, optional)
Compute the mean apparent diffusion coefficient (ADC) of the diffusion tensor.
ex. True
- get_cl (a boolean, default value is False, optional)
Compute the linearity metric of the diffusion tensor (one of the three Westin shape metrics).
ex. False
- get_cp (a boolean, default value is False, optional)
Compute the planarity metric of the diffusion tensor (one of the three Westin shape metrics).
ex. False
- get_cs (a boolean, default value is False, optional)
Compute the sphericity metric of the diffusion tensor (one of the three Westin shape metrics).
ex. False
- get_fa (a boolean, default value is True, optional)
Compute the fractional anisotropy (FA) of the diffusion tensor.
ex. True
- get_rd (a boolean, default value is False, optional)
Compute the radial diffusivity (RD) of the diffusion tensor.
ex. False
- get_value (a boolean, default value is False, optional)
Compute the selected eigenvalue(s) of the diffusion tensor.
ex. False
- get_vector (a boolean, default value is True, optional)
Computethe selected eigenvector(s) of the diffusion tensor.
ex. True
Outputs parameters:
- ad_file (a pathlike object or string representing a file, optional)
Output AD file
ex. '/home/username/data/derived_data/DWI_dti_ad.mif'
- adc_file (a pathlike object or string representing a file, optional)
Output ADC file
ex. '/home/username/data/derived_data/DWI_dti_adc.mif'
- cl_file (a pathlike object or string representing a file, optional)
Output linearity metric file
ex. '/home/username/data/derived_data/DWI_dti_cl.mif'
- cp_file (a pathlike object or string representing a file, optional)
Output planarity metric file
ex. '/home/username/data/derived_data/DWI_dti_cp.mif'
- cs_file (a pathlike object or string representing a file, optional)
Output sphericity metric file
ex. '/home/username/data/derived_data/DWI_dti_cs.mif'
- fa_file (a pathlike object or string representing a file, optional)
Output FA file
ex. '/home/username/data/derived_data/DWI_dti_fa.mif'
- rd_file (a pathlike object or string representing a file, optional)
Output RD file
ex. '/home/username/data/derived_data/DWI_dti_rd.mif'
- value_file (a pathlike object or string representing a file, optional)
Output selected eigenvalue(s) file
ex. '/home/username/data/derived_data/DWI_dti_value.mif'
- vector_file (a pathlike object or string representing a file, optional)
Output selected eigenvector(s) file
ex. '/home/username/data/derived_data/DWI_dti_vector.mif'
Useful links: