[RESOLVED] Running HCP pipeline on patient with large stroke lesion on one hemisphere

Dear Jure and Lining, and other experts:

I was wondering if there is work around for running HCP pipeline on subjects with large lesion, such as stroke, in one hemisphere?

I tried and the entire pipeline is stuck at the hcp_freesurfer stage.

Any advice would be greatly appreciated. Thank you very much as always.


Hi Ed,

There are two options here:

  1. The lesion is too severe and the data is useless. Here, we remove the problematic session from the study. Sadly, sometimes this has to be done.
  2. Use HCP FreeSurfer, recon_all manual edits. There is a parameter in QuNex called --hcp_fs_extra_reconall which you can use to set any recon_all parameters. See hcp_freesurfer — QuNex documentation and Edits - Free Surfer Wiki for additional details. Unfortunately, no one on our team considers themselves as an expert in FreeSurfer manual edits. If the information on the page I provided is not enough, maybe you can try asking around on the HCP board or with some FreeSurfer experts. If there are any issues with passing relevant parameters from QuNex to recon_all let me know and I will help out.

Best, Jure

Hi Jure:

Many thanks for the suggestions indeed.

I will explore a bit the recon_all manual edits then.

Thanks so much!