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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