Re: [Freesurfer] cortical surface area measurement and vertex-wise analysis

Hi Emma, I might not be the only one who is unsure what you mean by a vertex-wise cortical surface area measure. Do you mean something like what is illustrated in figures 2 and 3 here: http://www.pnas.org/content/107/29/13135.figures-only … which is similar, but not identical to the local gyr

[Freesurfer] cortical surface area measurement and vertex-wise analysis

Dear Freesurfers, I recently heard that there are several disadvantages to using a measure of cortical surface area in Freesurfer, specifically due to conducting a vertex-wise analysis. Can someone help me understand why a measure of surface area using this approach might be flawed? Thanks! ___

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

Re: [Freesurfer] Image normalization and pial/wm error

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.

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 h

Re: [Freesurfer] Image normalization and pial/wm error

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 brainma

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 sur

Re: [Freesurfer] WM & Pial Segmentation Errors

glad to hear it Bruce On Fri, 10 Oct 2014, Smith, Michael wrote: We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again! -Original Message

Re: [Freesurfer] WM & Pial Segmentation Errors

We re-ran that subject and it seemed to fix the problem, thanks! We will test it out on the other subjects with the same issue and see how that goes, but it looks like everything is good. Thanks again! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-b

Re: [Freesurfer] rawfunc2surf-sess with a limited set of surface files

No, use fmc.sm2.F99.lh.iter05 On 10/10/14 1:55 AM, Reza Rajimehr wrote: > Thanks Doug! I got it to work. The outputs are like > fmc.sm2.F99.lh.iter05.nii.gz > > Should I still specify stem as fmc.iter05 in mkanalysis-sess? > > Reza > > > Try added something like "-expkey iter05". When you make th

Re: [Freesurfer] excluding labels

Hi,I would like to exclude areas which were incorrectly segmented and could not be corrected after editing and re-running recon-all from the cortical thickness measure. Thank you again.Best,ruthiOn 09 Oct 2014, at 19:57, Douglas Greve wrote: What analys