Hi Antonella,

When saving wm edits, you don't need to save it as a different file. FreeSurfer will recognize your edits under wm.mgz. You then can run

recon-all -autorecon2-wm -autorecon3 -s NPI001

If you want to save a copy of the original wm.mgz, you can rename that (i.e. wm_orig.mgz).

-Khoa

On Tue, 19 Jul 2011, Antonella Kis wrote:

Hi Bruce,

Based on your last suggestion, after running the recon-all on my NPI001 subject:

recon-all -s NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001.nii.gz -qcache -all

and editing the wm, I saved all my edits (using the tool box menu as Save Volume As) under wm_edits_before.mgzm and I checked to make sure the edits are there/saved.

Now I need to run autorecon2-wm and autorecon3 and I am not sure if in the subjid I still need to write NPI001 (in this case how Freesurfer knows that my wm edits are in the wm_edits_before) or I need to run the following syntax: recon-all  -autorecon2-wm   -autorecon3-s  NPI001 -i /usr/local/freesurfer/subjects/june2011/_orig_/NPI001/mri/wm_edits_before.mgz ?

Thank you very much. Antonella