Re: [Freesurfer] white and pail surface editing

Hi Ri

I think you can just run it all as one recon-all command.

cheers Bruce On Mon, 18 Jul 2016, Ritobrato Datta wrote:

Hi All,

We have some subjects who have both wm errors and gm errors.

Is the following workflow possible

Step 1) control points for the white matter edits. DONT RUN recon-all

Step 2) add the pial surface edits. DONT RUN recon-all

Step 3) Run recon-all to incorporate control points for wm edits (recon-all -autorecon2-cp -autorecon3 -subjid cp_before)

AFTER step 3 is COMPLETE, run

Step 4) Run recon-all to create a fixed pial surface (recon-all -autorecon-pial -subjid pial_edits_before)

OR

Can step 3 and Step 4 be run together as recon-all -autorecon2-cp -autorecon-pial -autorecon3 -subjid cp_before

Please let me know.

Thanks

Ri _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer