Hi Guang, hard to say from just images, but it looks like those voxels are a lot darker than the rest of the gray matter. Did you visualize the surfaces? They may be voxels that contain a bunch of csf - if you look at them in another plane you could tell.
cheers, Bruce On Wed, 31 Mar 2010, Guang Zeng wrote: > > Hi, there, > > I have a scan which FreeSurfer skull-stripping gave me a bad brainmask (see > fig. 1). > I created a brainmask by using SPM segmentation results, then converted it to > FreeSurfer format with --conform flag on. > Finally, I masked T1.mgz using this brainmask, and I used it as my > brainmask.mgz (see fig. 2) to run the rest part (-autorecon2 -autorecon3) > > However, when I loaded the new aseg.mgz, I found that lots of boundary > voxel were not labled (see fig. 3) > > Anyone can give me some suggestions to fix this problem? Thanks a lot! > > Guang > > > > _________________________________________________________________ > Hotmail is redefining busy with tools for the New Busy. Get more from your > inbox. > http://www.windowslive.com/campaign/thenewbusy?ocid=PID27925::T:WLMTAGL:ON:WL:en-US:WM_HMP:032010_2 _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
