That makes life so easy! Thanks Douglas.
Cheers,
Zhivago...
On Tue, Jan 24, 2017 at 1:03 AM, Douglas N Greve <gr...@nmr.mgh.harvard.edu>
wrote:
> Yes. Easiest way it probably in matlab.
>
> Read in a surface overlay to use as a template
>
> overlay = MRIread('SUBJECTS_DIR/subject/surf/lh.w-g.pct.mgh');
>
> overlay.vol = yourdata;
> MRIwrite('lh.yourdata.mgh')
>
>
>
> On 01/20/2017 11:13 PM, Zhivago wrote:
> > Hi,
> >
> > If I know the activation values at each vertex/face of a surface, can
> > I create an mgh file independent of mri_vol2surf and overlay it on any
> > other surface or view it independently?
> >
> > Cheers,
> > Zhivago...
> >
> > On Thu, Jan 19, 2017 at 8:28 AM, Zhivago <zhiva...@gmail.com
> > <mailto:zhiva...@gmail.com>> wrote:
> >
> > Thanks a lot, Bruce.
> >
> > Cheers,
> > Zhivago...
> >
> > On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl
> > <fis...@nmr.mgh.harvard.edu <mailto:fis...@nmr.mgh.harvard.edu>>
> > wrote:
> >
> > 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 <mailto: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
> > <mailto: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
> > <mailto: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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> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> gr...@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
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>
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