Thanks again, yes that's what it looks like, but I just have one concern, if I have to manually edit dura and wm in all the slices and in most of the subjects, will it still give me reliable cortical thickness measure?
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 2:30 PM To: Freesurfer support list Subject: Re: [Freesurfer] Image normalization and pial/wm error Hi Sneha then I think manually editing is your best bet (sorry) Bruce On Fri, 10 Oct 2014, Sneha Pandya wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
