Hi Antonella,
you need to save the edits in the file wm.mgz, not rename it, otherwise recon-all won't be able to find it. Then run recon-all with -autorecon2-wm and autorecon3, but without the -i.
cheers Bruce 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