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...
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