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PennLINC / qsirecon

Reconstruction of preprocessed q-space images (dMRI)
https://qsirecon.readthedocs.io/
BSD 3-Clause "New" or "Revised" License
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Structural connectivity based on individual parcellations #27

Open LuRoe7 opened 1 year ago

LuRoe7 commented 1 year ago

Dear QSIPrep-Team, first of all: great pipeline, great work! We'll use it for all our upcoming DTI analyses!!

I was wondering if there is the option to use subject-specific parcellations as inputs to compute the structural connectivity matrices per participant? Or in other words: Is it possible to provide a specific individualized atlas for every subject?

Best,

Lukas

mattcieslak commented 1 year ago

Hi Lukas,

It's possible but would require so much reverse engineering that I wouldn't recommend attempting it. Which recon workflow were you planning on running? It may be easier to use custom atlases on qsiprep-preprocessed datasets via scripts

LuRoe7 commented 1 year ago

I'm using the mrtrix_multishell_msmt_ACT-hsvs workflow. But I'll think of the option to use the preprocessed files from QSIprep and to write a custom script to compute the SC matrices based on individualized parcellations.

mattcieslak commented 1 year ago

Did this end up working out for you? I think it's the best way to go in your case

LuRoe7 commented 1 year ago

Yes, it works!