Thanks a lot, Bruce. Cheers, Zhivago...
On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: > Hi Zhivago > > tksurfer is deprecated and uses one of the methods available in > mri_vol2surf, so our advice would be to use vol2surf > > cheers > Bruce > On Wed, 18 Jan 2017, Zhivago wrote: > > [cleardot.gif] >> >> Hi, >> >> From whatever I read, there seem to be 2 ways for overlaying activation >> maps >> on surfaces. >> >> 1) automatic/manual registration of activation volume to orig.mgz and >> usage >> of mri_vol2surf to create the overlay, say ?h.sig.mgh, which can then be >> overlaid on an inflated surface in freeview or tksurfer using the >> register.dat. >> >> 2) automatic/manual registration of activation volume to orig.mgz and >> overlay the activation volume on the inflated surface in tksurfer using >> the >> register.dat >> >> I want to know if both these are valid methods and if so, what are the >> pros >> and cons of each. Seems like mri_vol2surf lets us decide what part of the >> volume should be projected on the surface using the projfac arguments. >> But >> the direct volume overlay in tksurfer doesn't provide that option. In >> that >> case what part of the volume is projected on to the surface? >> >> Thanks, >> Zhivago... >> >> On Sun, Jan 15, 2017 at 10:12 PM, Zhivago <zhiva...@gmail.com> wrote: >> Thanks Bruce! Appreciate all the help, >> >> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> wrote: >> 1) This is up to you. Jon Polimeni had a nice paper >> describing the trade-off between accurately representing >> the local neural response (which is best at the white >> border) and statistical power (which is best nearer the >> pial surface). >> >> 2) This is also up to you.Read the help in mri_vol2surf. >> e.g.: >> >> mri_vol2surf --help >> . >> . >> . >> --projfrac-avg min max del : average along normal >> >> 3) it is the way that we support. >> >> cheers >> Bruce >> >> >> On Sun, 15 Jan 2017, Zhivago wrote: >> >> Hey Bruce, >> >> Thank you very much for the responses! Had >> posted a couple of more >> questions, but looks like it hasn't gone >> across. Will really appreciate it >> if you can provide some answers to these. >> >> 1) The mri_vol2surf is used to project the >> activations from the GM onto an >> inflated surface, which is usually the >> inflated smoothwm surface output from >> reconall. Will it be more accurate to use the >> inflated version of the >> intermediate surface, like halfway between the >> white and pial matter? Will >> it make any kind of sense? >> >> 2) When mri_vol2surf projects a volume to a >> surface, does it average the >> activation values of voxels along the cortical >> depth or sum it? What really >> happens beneath? Any amount of insight will >> be helpful. >> >> 3) Is mri_vol2surf the only way to view >> activation maps on inflated surfaces >> or any surface? >> >> Cheers, >> Zhivago... >> >> On Sun, Jan 15, 2017 at 9:23 PM, Bruce Fischl >> <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Zhivago >> >> 1) You can project from inside the >> ?h.white surface if >> projfrac<0 and outside pial if >> projfrac>1. <<0 and >>1 won't >> make much sense though as it starts to >> get arbitrary. >> >> 2) The default projfrac, as documented >> in the -help response, is >> 0. >> >> 3) Yes, 0-->white matter boundary. 1--> >> pial boundary. >> >> 4) The .mgh/.mgz file create by vol2surf >> is an nvertices x 1 x 1 >> vector, which is a scalar field over the >> surface. >> >> cheers >> Bruce >> >> >> >> On Sun, 15 Jan 2017, Zhivago wrote: >> >> Hi, >> >> >> I do not have a good understanding >> of the >> mri_vol2surf command. >> >> 1) Can this only project the part >> of the volume that >> lies between the white >> & pial matter? >> 2) What is the default projection >> parameter that it >> uses? >> 3) Does projection always start >> from the white >> matter, i.e. is 0 the white >> matter surface? >> 4) What is the nature of the mgh >> file that is >> created by: >> mri_vol2surf --src >> mri/spmT_0002.img --regheader >> s04 --interp nearest >> --hemi lh --o lh.sig.mgh >> >> Thanks, >> Zhivago... >> >> >> _______________________________________________ >> 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. 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