Re: [Freesurfer] Combining FS commands

Hi Erik

you can do this with the expert options in recon-all. Run recon-all -help and see if it is clear, otherwise post and someone here who has used it can walk you through it.

cheers Bruce

On Tue, 11 Feb 2014, Erik Lindberg wrote:

Dear Freesufers,

I want to run: mri_normalize gentle,

And

mris_make_surfaces min_border_white 85 -min_gray_at_white_border 80

In as few steps as possible as I will run around 800 images. So far I only managed to this by braking up the process several subparts (like doing autorecon1 before mri_normalize, and autorecon2 before mris_make_sufaces

If this could be combined somehow it would of course be a lot easier than running step by step 800 times.

Thanks in advance

Erik