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sina-mansour / UKB-connectomics

This repository will host scripts used to map structural and functional brain connectivity matrices for the UK biobank dataset.
https://www.biorxiv.org/content/10.1101/2023.03.10.532036v1
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Storage formats for exported intermediate data #23

Closed Lestropie closed 2 years ago

Lestropie commented 2 years ago

  1. If tractograms are to be provided with just streamline endpoints, the .tck format is highly sub-optimal: it stores a NaN triplet as a delimiter between streamlines, so with exactly two vertices per streamline it increases storage by 50%.

  2. Quantitative values per streamline are currently stored in ASCII form. Using binary floating-point (with a guaranteed endianness) would require less space. For fixel data we actually just use .mif images that are 1D, and that permits flexible endianness and memory-mapping; we could do that here, or something different. But either way, it may require some development at the MRtrix3 end to allow using those data as input to tck2connectome.

sina-mansour commented 2 years ago

This is now implemented so that the endpoints from tractograms and all quantitative values per streamlines are stored as NumPy binaries (NPY).