Hi, If I know the activation values at each vertex/face of a surface, can I create an mgh file independent of mri_vol2surf and overlay it on any other surface or view it independently?
Cheers, Zhivago... On Thu, Jan 19, 2017 at 8:28 AM, Zhivago <zhiva...@gmail.com> wrote: > 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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