proc_tract
Further details can be found in the Structural Connectomes section (-SC) of micapipe's ReadTheDocs.
Structural connectomes are generated with Mrtrix3 from pre-processed DWI data from the previous module and subcortical and cerebellar parcellations are non-linearly registered to native DWI space. First, a tractography with 40 million streamlines (default but modifiable, maximum tract length=400, minimum length=10, cutoff=0.06, step=0.5) is generated using the iFOD2 algorithm and 3-tissue anatomically constrained tractography (Smith et al., 2012; Tournier et al., 2010). A second tract density image (TDI) of the resulting tractography is computed for QC. By default, the full brain tractography is erased at the end of this module but can be kept using the option “-keep_tck”. Next, spherical deconvolution informed filtering of tractograms [SIFT2 (Smith et al., 2015a)] is applied to reconstruct whole brain streamlines weighted by cross-sectional multipliers. The reconstructed cross-section weighted streamlines are then mapped to each parcellation scheme, with (i) cortical, (ii) cortical and subcortical, and (iii) cortical, subcortical, and cerebellar regions (Smith et al., 2015b. These are also warped to DWI native space. The connection weights between nodes are defined as the weighted streamline count, and edge length matrices are also generated.
This image allows to perform a quick visual quality control of a connectome structural architecture and integrity.
