Re: [Freesurfer] incorrect GM/WM surfaces

2011-03-31 Thread Daniel G Wakeman
Hi Mayuresh, I assume you are talking about the area in the posterior midline, where the pial surface seems to go 'squiggly'. You also seem to have a problem with the right hemisphere (left visually: I hate radiology ;)), where some dura seems incorrectly labeled as pial surface (although the g

[Freesurfer] generate mask

2009-10-16 Thread Daniel G. Wakeman
Hi, I need to generate a mask from a 'BEM' surface (10242 vertices). I have tried doing this utililzing mri_surf2vol; however, this doesn't produce a good mask as only the vertices are utilized creating a speckled volume. Is there any way to create a proper mask utilizing all of the surfac

[Freesurfer] Wiki Request

2007-08-14 Thread Daniel G. Wakeman
Hello, I would like to request that the Freesurfer wiki be added to the interwiki map (see link below). This would streamline linking for individual lab's wikis to pages on the freesurfer wiki of commands (for example). Dan http://meta.wikimedia.org/wiki/Interwiki_map _

[Freesurfer] surfaces

2006-12-20 Thread Daniel G. Wakeman
Hi freesurfers, I have a question. I deleted some of the optic nerve on a participant and ran source /usr/local/freesurfer/nmr-std-env cd /space/doodles/3/users/dwakeman/pilot/again setenv SUBJECTS_DIR `pwd` recon-all -autorecon2-wm -autorecon3 -subjid p001 -mail dwakeman When the surfaces were