Hi Paul, Make smart cuts to simplify the normalization and skullstrip steps. This is done using tkmedit --> tkmedit monkey orig to open the volume, and then selecting --> Tools > Volume > Smartcut after positioning the cursor (red cross) at the desired location. Smart cuts are only orthogonal and calculated as follow: if the cursor is in the upper half of the volume, everything above the cursor will be removed; if the cursor is in the right half of the volume, everything to the right will be removed, etc. It is not necessary to strip all the skull (and may not be necessary to strip any of the skull); the point is only to disrupt the skull to make the strip process more effective.
Reza > Hello All, > > I am having a very difficult time getting skullstrip to work on my monkey > anatomical data set. Are there any suggestions on how to get it to work > properly? > > Thanks in advance > > Paul > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ******************************** Reza Rajimehr, MD NMR Athinoula A. Martinos Center Department of Radiology Massachusetts General Hospital (MGH) Building 149, 13th St. Charlestown, MA 02129 Email: [EMAIL PROTECTED] ******************************** _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
