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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