External Email - Use Caution I would add that a properly eroded WM mask is not very effective for fMRI denoising at least relative to spatial and temporal ICA-based denoising. An uneroded mask behaves similarly to global signal regression, which removes both global noise and global neural signal.
Matt. On 8/7/18, 4:22 PM, "[email protected] on behalf of Bruce Fischl" <[email protected] on behalf of [email protected]> wrote: >1. You can dig up our old 1999 recon papers if you are really interested. >Lots of segmentation techniques are not probabilistic. > >2. Again, we don't output probabilities. YOu are better off eroding as >Matt >suggested. > >3. mris_fill fills the interior of a surface - nothing to do with >mri_fill. > >If all you want is a nuisance regressor just take the wm.mgz, or interior >of the white surface and erode it once, then use those voxels >Bruce > > >On Tue, 7 Aug 2018, Ben M wrote: > >> >> External Email - Use Caution >> >> Hi Bruce, >> >> Thank you very much for your reply. The idea is to create a WM mask >>that I can use for the denoising >> step of resting state connectivity analysis. Do you mind if I ask you a >>few follow up questions? >> >> 1 - "our primary cortical segmentation of the wm is not probabilistic." >> How is the segmentation of the WM achieved in freesurfer then, if not >>probabilistic? >> >> 2 - "In any case you want partial volume fractions I expect, not >>posterior probabilities." >> Sorry, I'm not sure what you mean by partial volume fractions. In >>several papers I have read the WM >> is first thresholded (eg p >.9) to ensure that only WM voxels are >>included in the mask, which is >> also eroded. Are the values being thresholded partial volume fractions >>then, and not probabilities? >> But if segmentation is done on tissue probability maps (eg like in SPM >>I think), wouldn't you have >> probabilities? Or do you mean you have partial volume fractions just in >>freesurfer? >> >> 3 - "I would use mris_fill to create a mask of the WM from the ?h.white >>surfaces, if you want the >> most accuracy" >> I found more information about the command mri_fill than mris_fill, is >>there a difference between >> the two, or can I use both for the same thing? >> >> Sorry for the newbie questions, I am just beginning using freesurfer. >> >> Best >> Ben >> >> On Tue, Aug 7, 2018 at 6:08 PM, Bruce Fischl >><[email protected]> wrote: >> Hi Ben >> >> our primary cortical segmentation of the wm is not probabilistic. >>In any case you want >> partial volume fractions I expect, not posterior probabilities. I >>would use mris_fill to >> create a mask of the WM from the ?h.white surfaces, if you want >>the most accuracy >> >> cheers >> Bruce >> >> On Tue, 7 Aug 2018, Ben M wrote: >> >> >> External Email - Use Caution >> >> Hi, >> I would like to create a mask of the WM for fMRI analysis. >>I read a previous >> post in which it was >> suggested to get the wm segmentation and erode it, since >>the result will be >> exclusively WM. My >> question is why is this so? Why can I assume that getting >>the WM mask from >> the aseg file will almost >> certainly get me high probability WM, >0.9 for example? In >>most segmentation >> algorithms we get >> posterior probabilities at each voxel, so that we can then >>select voxels >> with posterior >> probabilities >0.90 for example. Why is freesurfer's WM >>segmentation so >> accurate that we do not need >> posterior probabilities? Are these very high probabilities >>somehow already >> coded in freesurfer's >> segmentation algorithm? >> Thanks, >> Ben >> >> >> _______________________________________________ >> 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. >> >> >> ________________________________ The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail. _______________________________________________ Freesurfer mailing list [email protected] https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
