Hello Freesurfer experts,
I have two separate questions.
1. I am doing an MRI study on young children (3-5 years old). I have read in a few a different places that Freesurfer isn't ideal for analyzing young subjects. It does seem to be processing my subjects just fine though, with the exception of needing a bit of editing on a few images. Out of curiosity, I would like to try using a different template to register my subjects to. I know Freesurfer uses an MNI based adult template, and I have acquired a template for my specific age group. Is it possible for me to replace the Freesurfer template with my own. How would I go about doing this, and do you expect the results I get to be better or worse than using the adult template.
2. When I do white matter edits, they seem to be getting overwritten when I rerun the subject. I am editing the wm.mgz volume, making sure that I save it, and then rerunning the following line
recon-all -s subject -autorecon2 -autorecon3
I've also tried running from different places in the pipeline (-autorecon2-cp, -autorecon2-wm) and it still does not work. Any idea whats going wrong here, and how I might fix this.
Greatly appreciate any help with this
Matt