Hi Stephanie, hmmm, that's pretty poor. Usually when you see the surfaces missing large chunks of white matter it means that there are topological defects that were incorrectly fixed. If you want to upload the subject we can take a look, or you can try fixing them yourself (there's a tutorial that covers this).
cheers, Bruce On Thu, 1 Apr 2010, Stephanie Biglarian wrote: > We're using Freesurfer version 4.5.0_64bit to delineate and calculate > cortical thickness. The images we are working with are poor quality and when > we run the Freesurfer program, we have problems with the segmentation of > prefrontal and temporal areas. We read through previous posts on the mailing > list and found that we should apply control points to normalize the white > matter on about 20 subjects and possibly use these to apply bias field > correction on the remainder. However, it seems that after multiple times of > applying control points (about 25 control points per subject) and running the > recon-all command, the problem is not corrected. The segmentation does not > extend to the farthest part of the temporal poles. The command we are using > is: > > recon-all -autorecon-all -autorecon2-cp -autorecon3 -subjid (subj) -sd > (directory) -no-isrunning > > Are there any better ways of going about this? I have attached screenshots > of one of the subjects in two different views. > _______________________________________________ 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.
