Bulk Download of Co-registered DTI and T1-weighted Brain Maps for White Matter Tract Analysis

Technical
1

Hello Allen Brain Map Community,

I’m trying to access DTI-weighted human brain maps from the Allen Brain Atlas that include white matter tract anisotropy data. I’m also looking for corresponding T1-weighted structural maps that clearly show the architecture and relative position of white and gray matter components.

My goal is to analyze white matter tract anisotropy in the context of surrounding brain structures, so need the DTI and T1 maps to be co-registered or aligned.

I’m hoping someone can guide me to the most appropriate data sources and download methods.

Is there a way to download the full dataset in bulk, rather than one slice at a time? Has anyone worked with this kind of data from Allen before and could share tips or processing scripts?

Details:

  1. DTI-weighted brain maps suitable for white matter tract anisotropy analysis, including:

    • Fractional anisotropy (FA) maps

    • Mean diffusivity (MD) maps

    • Principal diffusion direction data

    • Raw diffusion tensor data if available

  2. T1-weighted brain maps that clearly delineate:

    • White matter tract architecture and relative positioning

    • Gray matter components and boundaries

    • High-resolution anatomical reference data

  3. Requirement: DTI and T1 datasets co-registered/aligned so that white matter tracts identified in the DTI analysis can be accurately mapped to the anatomical structures visible in the T1 images.

I have more questions.

Do specific Allen Brain Atlas projects contain both DTI and T1 data? Are co-registered datasets available, or would I need to perform the registration myself?

Are there technical documentation or whitepapers describing DTI acquisition parameters and processing? Maybe file formats or datasets optimal for white matter tract modeling applications?

Any guidance on accessing these resources would be greatly appreciated. Thank you for maintaining such valuable open science resources!

Best regards,

Brian Michael Coyle

2

Thank you for your email. We currently do not have anyone on staff who works in this area or who has the technical expertise to answer your questions.

Thank you

3

The closest thing to a centralized repository for Neuroimaging that we have at the Allen Institute is this page: Toolkit - brain-map.org. If the information you want is not here, then we would encourage other community members to respond, or you could reach out to manuscript authors.

4

Thank you for the link. For this project, I ended up using the UMinn HCP dataset instead, as it was immediately available and fit my needs for high-resolution structural and diffusion data. I keep Allen in mind for future stages.
Brian