Preprocessing for Kong 2022 areal-level MS-HBM pipeline

[kianal...@gmail.com]

Dear CBIG team,

Our supercomputing system was recently upgraded to RHEL 9, and unfortunately, none of the currently available AFNI versions are compatible with this OS. As a result, we’re unable to run the CBIG 2016 preprocessing pipeline, which relies on AFNI functions.

Given this constraint, I’m exploring alternative preprocessing options. Would it be feasible to use a pipeline like fMRIPrep to preprocess the data, then project the outputs to the surface for use with the Kong 2022 areal-level MS-HBM pipeline? If so, are there additional conversion or formatting steps required to make the data compatible?

I'm open to other solutions as well, let me know what you think! 

[Aihuiping Xue]

Hi,

If AFNI is unavailable for you, you can remove the deoblique step in config. Please let us know if you still cannot run our preprocessing pipeline. 

Best Regards,

XUE Aihuiping

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[kianal...@gmail.com]

I ran the deoblique step within an AFNI container first, and was able to run all the rest the steps as intended. 

Thank you for your help! Sincerely,

Kiana