Hi Ali

No, there is no auto-cutting. You need to cut your own patch

Bruce

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Alison McDonnell
Sent: Tuesday, November 30, 2021 2:01 PM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
Subject: [Freesurfer] FREESURFER issue making flatmap

        External Email - Use Caution        

hi all, 

I was trying to open the inflated version after running recon all so i could make a patch and then make flatmap. when i  ran 

mris_flatten lh.full.patch.3D lh.full.flat.patch.3D 

it gave an error saying there was no such file but i thought it should have been generated by recon all. them i just tried to open using freeview amd it said it couldnt determine the file type. if anyone has any idea whats going on that would be great. ive attached screenshot of the terminal showing the error messages and what i tried to do. it also took a very long time to run recon all but then ended with no errors so i dont know what problems came up then. 

thanks, Ali