Re: [Freesurfer] using -bigventricles flag in FS 5.3

Hi Mehul

yes, if you are using it you should always include it on the recon-all command line

cheers Bruce On Sun, 5 Feb 2017, Mehul Sampat wrote:

Hi Folks,

I have a question about the usage of the -bigventricles flag in FS 5.3.

1. Suppose i run recon-all with -bigventricles option.
2. Then i add control points and run recon-all with the -autorecon2-cp as described in the recon-all

help. USAGE: recon-all 3. The recon-all help mentions "-autorecon2-cp : process stages 12-23 (uses -f w/ mri_normalize, -keep w/ mri_seg"

My question is: when i run recon-all the second time with the -autorecon2-cp flag, do i need to include the -bigventricles option again ?  In general, if the first round of processing used  -bigventricles, should it be always used if recon-all is re-run after making edits ?

Thanks Mehul ps: can you believe the Patriots won SB51 !! :-)