ConstrainedSphericalDeconvolution brick¶
Estimate fibre orientation distributions (FOD)¶
Create Fiber Orientation Densities (FOD) using the basis functions generated by the ResponseSDDhollander brick.
The aim is to estimate the amount of diffusion in each of three orthogonal directions. The FOD are estimated using spherical deconvolution.
(mrtrix dwi2fod 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 string representing an existing file)
Input DWI image (valid extensions: [.mif]).
ex. '/home/username/data/raw_data/DWI.mif'
- wm_txt (a string representing an existing file)
WM (white matter) response text file, for example from ResponseSDDhollander brick.
If csd algorithm is used, this file should only contain a a single row, corresponding to the b-value used for CSD. If msmt_csd algorithm is used, this file should have a number of rows equal to the number of b-values used.
ex. '/home/username/data/derived_data/DWI_response_wm.txt'
Optional inputs with default value parameters:
- algorithm (csd or msmt_csd, optional, default value is msmt_csd, optional)
- The algorithm to use for FOD estimation.- csd: perform single-shell single-tissue CSD. This algorithm only uses a single b-value.- msmt_csd: perform multi-shell multi-tissue CSD. This algorithm requires at least one unique b-values for each tissue compartiment to estimate.
ex. csd
- get_predicted_signal (a boolean, default value is False, optional)
Get a file with the predicted signal from the FOD estimates (only for msmt_csd algorithm)
ex. False
Optional inputs parameters:
- csf_txt (a string representing an existing file, optional)
CSF (Cerebrospinal fluid) response text file, for example from ResponseSDDhollander brick.
If msmt_csd algorithm is used, this file should have a number of rows equal to the number of b-values used.
ex. '/home/username/data/derived_data/DWI_response_csf.txt'
- gm_txt (a string representing an existing file, optional)
GM (grey matter) response text file, for example from ResponseSDDhollander brick.
If msmt_csd algorithm is used, this file should have a number of rows equal to the number of b-values used.
ex. '/home/username/data/derived_data/DWI_response_gm.txt'
- in_mask (a string representing an existing file, optional)
Mask image in order to only perform computation within this specified binary brain mask image
ex. '/home/username/data/derived_data/DWI_brainmask.mif'
- in_directions (a string representing an existing file, optional)
A text file containing [ az el ] pairs for the directions over which to apply the non-negativity constraint (if not set, the built-in 300 direction set is used).
ex. '/home/username/data/derived_data/directions.txt'
- max_sh (a list of items which are an integer, optional)
Maximum harmonic degree of response function (one by shell). If omitted, the command will use the lmax of the corresponding response function (i.e based on its number of coefficients), up to a maximum of 8.
ex. [3, 3, 3]
- shell (a list of items which are a float, optional)
Specify one or more b-values to use during processing.
ex. [1000.0, 3000.0]
Outputs parameters:
- wm_odf (a pathlike object or string representing a file)
Out WM ODF.
ex. '/home/username/data/derived_data/DWI_wm_odf.mif'
- gm_odf (a pathlike object or string representing a file, optional)
Out GM ODF.
ex. '/home/username/data/derived_data/DWI_gm_odf.mif'
- csf_odf (a pathlike object or string representing a file, optional)
Out CSF ODF.
ex. '/home/username/data/derived_data/DWI_csf_odf.mif'
- predicted_signal_file (a pathlike object or string representing a file, optional)
Out predicted signal.
ex. '/home/username/data/derived_data/DWI_odf_predicted_signal.mif'
Usefull links: