Hi,
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
Thanks Bruce! Appreciate all the help,On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl <fischl@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 <fischl@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...
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