Mathias Goncalves

Yep, unless FastSurfer changes its outputs to follow the same structure of FreeSurfer recon-all (or provides a flag to allow you to do this), this is going to require generating...

Hi @ly6ustc , Are you processing the same data you are comparing within the HCP database? This may be related to https://github.com/nipreps/fmriprep/issues/2333 - two things to that come to mind:...

Thanks for following up - I'm unsure if this is a bug or a limitation. fMRIPrep's version of CIFTIs have a few notable differences from ones generated by HCP Pipelines:...

At first glance, that looks correct - the only suggestion I would have is if you are comparing with the CIFTI surfaces, you will want to ensure the surfaces share...

hi @switt4, sorry for the delay - can you post the contents of the crashfile located at `/scratch/switt4/Undergrads_fMRI/TAR/fmriprep/fmriprep_20.2.6/sub-001/log/20211108-142242_3b3ca22e-c13c-42e4-bab7-ddf7d5a42849/crash-20211108-142348-sw...`

It seems you are hitting a wall with the `--use-syn-sdc` pathway of the workflow - I would avoid using that flag with your data for the time being. If you...

Are there any subjects in the dataset where the SyN correction worked as expected?

Good to hear - the `--use-syn-sdc` flag is still fairly experimental, so I can't say I'm surprised about these discrepancies. Do you know if there is something different (scanning parameters,...

This looks like a case of a stale working directory - can you try rerunning with a fresh one?

If you add the run label to your BIDS data, it should carry over to the fMRIPrep derivatives. I would lean towards leaving this up to the user rather than...