It is is really bright there, try putting a few control points in WM (make sure they are in WM)
On 3/3/20 12:30 PM, Laboratorio de Neurociencia Funcional wrote: > > External Email - Use Caution > > Dear Freesurfeer experts, > After running the recon-all in one of my subjets, part of the temporal lobe > was partially excluded. Then, I tried to use the watershed algorithm to be > less agressive in the skull stripping > as follows: > > recon-all -skullstrip -wsthresh 35 -clean-bm -no-wsgcaatlas -subjid sub_001 > > The problem was solved in the brainmask.mgz but not in the cortical surfaces. > To > handle this issue, I edited the white matter and run the recon-all > -autorecon2-wm > -autorecon3 without success. I also placed control points but the following > error appeared after running > the recon-all -autorecon2-cp -autorecon3: > > recon-all -s sub_001 existed with errors > > I noted that white matter of this part of the temporal lobe has high values > (up to 132). What can I > do to solve the problem with this subject? > > Thank you in advance. > > Best regards, > Marina > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
