You only ran it through -autorecon1, rerun with -all or with -autorecon2 -autorecon3 to generate all the files
On 3/17/2020 12:31 PM, Alexander Barnett wrote:
External Email - Use Caution
Hello FreeSurfer Developers,
I am trying to inspect the white matter gray matter surface to verify its accuracy as described in (http://freesurfer.net/fswiki/FsTutorial/ControlPointsV6.0). When I try to open freeview freeview -v 101/mri/brainmask.mgz \ -f 101/surf/lh.white:edgecolor=yellow I get an error that says it Failed to load Surface 101/surf/lh.white. The brainmask.mgz opens fine. When I looked in the /101/surf/ folder, I see lh.white.H, lh.white.K, lh.white.preaparc, lh.smoothwm, but there is no lh.white file. When I inspect the ReconAll table (https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0) I see that there is no step that creates ?h.white files in V6.0 (note: there is a step that will make lh.white in V5.3).
How can I properly assess the white matter gray matter surface in V6.0?
- FreeSurfer Version: freesurfer-i386-apple-darwin11.4.2-stable6-20170119
- Operating system : MacOS High Sierra version 10.13.6
- recon-all.log: see attached
ReconAllTableStableV6.0 - Free Surfer Wiki https://surfer.nmr.mgh.harvard.edu/fswiki/ReconAllTableStableV6.0 This table shows the recon-all steps for the stable, publicly released, version 6.0 of FreeSurfer (available here).. See also the OtherUsefulFlags for other recon-all options. surfer.nmr.mgh.harvard.edu
Alex Barnett, PhD
Postdoctoral Scholar
UC Davis, Center for Neuroscience
Dynamic Memory Lab
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer