QSIRecon: construct connectivity matrices based on a custom atlas for each individual

[Steven]

Hi @angelwong,

@angelwong

~/Software/singularity_images/qsirecon-26.0.0.sif

You are going to want to update 26.0.1 to make connectivity matrices (Release 26.0.1 · PennLINC/qsirecon · GitHub).

@angelwong

How can I incorporate this custom atlas into the reconstruction workflow for each individual? Can you show me the steps?

You may find this post helpful: QSIRecon Custom Atlas and Response Functions - #3 by tsalo

@angelwong

Will this additional step (constructing connectivity matrices) start from scratch? Or will it build on the existing reconstructed files from QSIRecon?

If you’ve only run ss3t_auto_track, then you will still need to generate whole-brain tractograms. The only thing that could be reused are the response functions / FODs. I forget if they are reused or rather regenerated in each run. I think you would need to have a same-name recon spec and same working directory for a chance to reuse those response functions / FODs. But the whole brain tractogram is much more time consuming anyway, so the time save won’t be too much, maybe ~1 hour per scan.

Best,
Steven