On Tue, Jan 24, 2017 at 1:03 AM, Douglas N Greve <greve@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 <zhivagoa@gmail.com
> <mailto:zhivagoa@gmail.com>> wrote:
>
> Thanks a lot, Bruce.
>
> Cheers,
> Zhivago...
>
> On Wed, Jan 18, 2017 at 7:01 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu <mailto:fischl@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

> <zhivagoa@gmail.com <mailto:zhivagoa@gmail.com>> wrote:
> Thanks Bruce! Appreciate all the help,
>
> On Sun, Jan 15, 2017 at 10:02 PM, Bruce Fischl
> <fischl@nmr.mgh.harvard.edu

> <mailto: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

> <mailto: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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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
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