White Matter Tracts

Before practicum on Friday, please complete the following:

White Matter Anatomy

• Reading: a review on recent known and unknown white matter pathways: Bullock DN, Hayday EA, Grier MD, Tang W, Pestilli F, Heilbronner S. A taxonomy of the brain’s white matter: Twenty-one major tracts for the twenty-first century.

• Video: Computational Neuroanatomy at DIPY Workshop

During practicum on Friday:

Review of the assignment 1 (10 min)

Introduction to white matter pathways (20 min)

source: Neuroimage. 2021 Dec 15;245:118651.

• Download and open HCP1065 Group-average template 1mm [download] (details) in Step T3
• Download and open tractography atlas [download] (details)
• simplified atlas and labels

• abbreviations

• White matter pathways can be catogorized into commissural, association, and prjection pathways.
  • Commissural pathways: pathways connecting left and right hemisphere
    • anterior commissure
    • corpus callosum
  • Association pathways: pathways connecting cortical regions to cortical regions
    • arcuate fasciculus (AF), frontal aslant (FAT), superior longitudinal fasciculus (SLF) II, III
    • cingulum (frontal parahippocampal, frontal parietal, parahippocampal parietal, parahippocampal, and parolfactory), superior longitudinal fasciculus (SLF) I
    • inferior fronto-occipital fasciculus (IFOF), uncinate fasciculus (UF)
    • inferior longitudinal fasciculus (ILF), middle longitudinal fasciculus (MdLF), vertical occipital fasciculus (VOF), temporo-parietal aslant tract, extreme capsule.

source: Nature communications. 2022 Aug 22;13(1):1-3.

• Projection pathways: pathways connecting cortical regions to the basal ganglia or brain stem nuclei
  • thalamus: thalamic radiation (anterior, posterior and superior), acoustic radiation, optic radiation, dentatorubrothalamic tract (DRTT), medial lemniscus
  • striatum: corticostriatal tract (anterior, superior, and posterior), fornix
  • brain stem nuclei: corticospinal tract, reticulospinal tract, corticobulbar tract, corticopontine tract (frontal, parietal, and occipital),

• Cerebellum pathways, brainstem pathways, cranial nerves

• White matter regions (not pathways)
  • internal capsule
  • corona radiata
  • centrum semiovale

Virtual dissection (20 min)

• Tract menu
  • Tract editing and shortcuts
  • Virtual dissection [document]
    • Difficulty level (easy): commissural pathways
    • Difficulty level (medium): association pathways
    • Difficulty level (hard): projection pathways
  • Region-based filtering

Automatic Fiber Tracking (10 min)

• Automatic fiber tracking [document]

Assignment: Download FIB file

1. Download 100206.src.gz.gqi.1.7.fib.gz and 100206_T1w.nii.gz

2. Open the FIB file using [Step T3 Fiber Tracking] and click on [Step T3d Tracts][Fiber Tracking] to generate whole brain tracts.

• [Optional] check out document and test different fiber tracking parameters. Observe how changing them leads to different results.

1. Manually segment left arcuate fasciculus, cingulum, uncinate fasciculus, corticospinal tract from whole brain tracks. Compare it with automatic tracking results.

2. Segment left arcuate fasciculus into the acoustic, visual, and lexical encoding part and assign different colors (reference: Giampiccolo D, Duffau H. Controversy over the temporal cortical terminations of the left arcuate fasciculus: a reappraisal. Brain. 2022 Feb 10.)

(Giampiccolo et al. 2022)

(Segmented on HCP1065 tractography atlas)