Hi Sneha it looks like it is grabbing a bunch of dura. Do you happen to have a hires T2 or flair image? If so, you can use that in recon-all postprocessing to remove the dura. If not you can try using the graph cuts skull stripping to get rid of some of it. I can't tell the accuracy of the surfaces in other locations in the images. Other than dura is it reasonably acurate? cheers Bruce
On Fri, 10 Oct 2014, Sneha Pandya wrote: > Dear all, > > I am running recon-all on few SPGR T1s and few MPRAGE T1s. However most of > my dataset, may it be SPGR or MPRAGE has some artifacts and poor wm/gm > contrast. Have attached a screen shot of bad pial and wm error (going beyond > dura). Even gcut did not do a good job of cutting of all the dura, and I had > to manually edit voxels in all the slices. I feel even after that if I run > recon-all, it will not give me any reliable cortical thickness measures. > > Can anyone please suggest me if I should still manually edit all other > subjects for all the slices throughout the volume or exclude them from > analysis? > > PS: attached image FOV is 260 and I used -cw256 flag to restrict FOV to 256. > For other images FOV is within 256, but still there is lot of dura in the > brainmask. > > Thanks, > Sneha > > > _______________________________________________ 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.
