Hi Bruce, Yes, there is a lot of dura. Unfortunately we do not have either flair or T2 as a reference to remove dura. I tried running gcut to cut off dura, it still won't help and I still had to manually edit whole volume to get rid of it. If it helps I can send you orig.mgz, nu.mgz and brainmask.mgz post graph cut to look at. However for other structures it is difficult to tell about the accuracy because I feel contrast is a little poor. Sequence of this subject is spgr with voxel size of 1.01mm*1.35mm*1.5mm(sl. thk), with 26FOV. I even used cw256 flag to restrict the field of view. So not really sure why is segmentation so poor.
Other subjects in this dataset has between 20 to 25FOV, and varying voxel size from 0.93*1.25*1.5 to 1*1*2. Thanks, Sneha _______________________________________ From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Friday, October 10, 2014 1:58 PM To: Freesurfer support list Subject: Re: [Freesurfer] Image normalization and pial/wm error 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 Freesurfer@nmr.mgh.harvard.edu 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. _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
