External Email - Use Caution
Hello team,
We have first fixed non-cortex voxels in the pial surface using the brainmask.mgz volume, and we next corrected pial surfaces that mistakenly included cerebellum by creating a copy of 'brain.finalsurfs.mgz' named 'brain.finalsurfs.manedit.mgz' and erase problematic voxels in it . All these changes appeared correctly in brain.finalsurfs.mgz after running autorecon-pial in the two steps.
How could I get a .nii file containing all these changes in the native space (0.65x0.65x0.65)?
Thank you!
Hi Sofia
you should be able to "reslice like" the rawavg.mgz:
mri_convert -rl rawavg.mgz brainmask.mgz brainmask.rawavg.mgz
you might also want to specify the interpolation as e.g. nearest with -rt nearest (trilinear is the default I believe) On Tue, 24 Jul 2018, Sofia Rodriguez Penuela wrote:
External Email - Use Caution
Hello team,
We have first fixed non-cortex voxels in the pial surface using the brainmask.mgz volume, and we next corrected pial surfaces that mistakenly included cerebellum by creating a copy of 'brain.finalsurfs.mgz' named 'brain.finalsurfs.manedit.mgz' and erase problematic voxels in it . All these changes appeared correctly in brain.finalsurfs.mgz after running autorecon–pial in the two steps.
How could I get a .nii file containing all these changes in the native space (0.65x0.65x0.65)?
Thank you!
-- Sofía Rodríguez Peñuela, Técnico de Laboratorio. Laboratorio de Neurociencia Funcional Departamento de Fisiología, Anatomía y Biología Celular. Universidad Pablo de Olavide Ctra. de Utrera, Km.1 41013 - Sevilla
- España -
Movil: 627273085 Email: srodpen@upo.es http://www.upo.es/neuroaging/es/
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Sofia Rodriguez Penuela