[Freesurfer] Two basic questions: brainmask file versions and qcache

External Email - Use Caution

Dear FreeSurfer experts,

I hope this email finds you all well.

I have two relatively basic questions that I am hoping to get some help with.

My basic planned processing pipeline is:

Run initial recon-all with gcut and ws flags

Edit white matter/pial voxels and add control points (as needed)

Run second recon-all with autorecon2 and autorecon3 flags

Run LGI

I have two questions about this:

When I run the initial recon-all, I end up with three versions of the brainmask within the /mri/ folder: brainmask.auto.mgz, brainmask.gcuts.mgz, brainmask.mgz. Which brainmask version do I edit, so that my edits are incorporated into the second recon-all run and thus the second attempt at wm/gm segmentation is better?

Exactly when and with what command(s) do I use the qcache flag?

I apologize that these are quite basic, but sincerely appreciate any input anyone might be able to provide.

Thank you so very much in advance!

All the best,

Emily Harriott

Doctoral student at Vanderbilt University