MRI

Images were collected with a spin echo DWI sequence. Typical parameters were: TR/TE=400ms/22ms, isotropic resolution 0.1mm to 0.1375mm. Multishell diffusion scheme with 3 or 4 shells with b-values 500-2000 s/mm2 was employed.

DSI Studio (http://dsi-studio.labsolver.org) The restricted diffusion was quantified using restricted diffusion imaging [1]. The diffusion data were reconstructed using generalized q-sampling imaging [2] with a diffusion sampling length ratio of 1. A deterministic fiber tracking algorithm [3] was used. A seeding region was placed at whole brain. The anisotropy threshold was set to eliminate background voxels (0.022-0.034). The angular threshold was 60 degrees. The step size was 0.06 mm. The fiber trajectories were smoothed by averaging the propagation direction with 20% of the previous direction. Tracks with length shorter than 0.5 or longer than 30 mm were discarded. A total of 2 seeds per voxel were placed in delineated regions of interest (220000-440000).

Regions of interest (ROIs) were used as the brain parcellation, and the connectivity matrix was calculated by using count of the connecting tracks. The connectivity matrix and graph theoretical analysis was conducted using DSI Studio (http://dsi-studio.labsolver.org). ROIs were determined manually from the nqa and iso images.

For comparison of connectivity across samples, the count of connecting tracks in the optic tract was set equal to 10000.

Following Chung et al [4] we define a Connectivity Strength Index (CSI) for each ROI as log10(count of connecting tracts). For the consensus connectivity we took the median of the CSI from the 3 samples with a lower bound of 1.5.

Visualization with JColorGrid [5] and chordiag [6]

  1. Yeh FC, Liu L, Hitchens TK, Wu YL. Mapping immune cell infiltration using restricted diffusion MRI. Magn Reson Med. 2017;77(2):603-12. Epub 2016/02/05. doi: 10.1002/mrm.26143. PubMed PMID: 26843524.
  2. Yeh FC, Wedeen VJ, Tseng WY. Generalized q-sampling imaging. IEEE Trans Med Imaging. 2010;29(9):1626-35. Epub 2010/03/23. doi: 10.1109/TMI.2010.2045126. PubMed PMID: 20304721.
  3. Yeh F-C, Verstynen TD, Wang Y, Fernández-Miranda JC, Tseng W-YI. Deterministic Diffusion Fiber Tracking Improved by Quantitative Anisotropy. PLOS ONE. 2013;8(11):e80713. doi: 10.1371/journal.pone.0080713.
  4. Chung WS, Kurniawan ND, Marshall NJ. Toward an MRI-Based Mesoscale Connectome of the Squid Brain. iScience. 2020;23(1):100816. Epub 2020/01/24. doi: 10.1016/j.isci.2019.100816. PubMed PMID: 31972515; PubMed Central PMCID: PMCPMC6974791.
  5. Joachimiak MP, Weisman JL, May BCH. JColorGrid: software for the visualization of biological measurements. BMC Bioinformatics. 2006;7(1):225. doi: 10.1186/1471-2105-7-225.
  6. Flor M. chorddiag 0.1.3 GitHub2020. Available from: https://github.com/mattflor/chorddiag/.