Hi Bruce,
Sure, shall try to do that comparison and see if it works. Also would specifying image intensity in the expert option help in any case.
Thanks, Sneha ________________________________________ From: freesurfer-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@nmr.mgh.harvard.edu] Sent: Friday, October 10, 2014 3:01 PM To: Freesurfer support list Subject: Re: [Freesurfer] Image normalization and pial/wm error
I don't really know, sorry. You could to an inter- and intra-rater test by editing some of the images twice On Fri, 10 Oct 2014, Sneha Pandya wrote:
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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fischl@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
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