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. 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. >>> >>> >>> >>> >> _______________________________________________ >> 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. 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. >> >> >
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