Automatic Bundle Segmentation

This section describes the integrated automatic virtual dissection of the main brain tracts based on auto_tracto. This tool was implemented using ANTs registration tools. The main purpose of the script 03_auto_tracts.sh is to split a tck tractogram into 35 white matter tracts, using already established automatic dissection protocols, which were manually tuned for optimal performance.

Derived from a full brain tractogram, 35 bundles are virtually dissected using the LANIREM protocols. The quality of the full brain tractogram will determine the quality of bundle separation. It is highly recommended to provide a tractogram with more than one million streamlines, and quality controlled for any errors. Strategies such as anatomically-contstrained tractography (ACT) and spherical deconvolution informed filtering of tractograms (SIFT), available in MRTrix3, should aid in obtaining such high-quality tractograms.

../../_images/autotract.png

  • Non-linear (SyN) registration of the native FA map to the FA atlas (FMRIB58_FA_1mm)

  • Apply transformation to each bundle protocol to register them to the native FA space (DWI)

  • Verify stop criterion conditionals

  • Filter each white matter bundle according to the dissection protocols

List of names and their acronyms obtained with the integrated automatic virtual dissection of the main brain tracts based on auto_tracto:

Acronym

Tract name

AC

Anterior Commissure

AF

Arcuate Fasciculus

CC_MID

Corpus Callosum middle portion

CGFP

Cingulum, fronto-parietal portion

CGH

Cingulum, parahippocampal portion

CG

Cingulum, whole

CGR

Cingulum, rostral and subgenual

CST

Corticospinal tract

FA

Frontal aslant

FMA

Forceps major of corpus callosum

FMI

Forceps minor of corpus callosum

FX

Fornix

IFOF

Inferior fronto-occipital fasciculus

ILF

Inferior longitudinal fasciculus

MLF

Middle longitudinal fasciculus

OR

Optic radiation

SLF

Superior longitudinal fasciculus

UF

Uncinate fasciculus

VOF

Vertical occipital fasciculus