Re: [Freesurfer] Registering T-maps to the inflated surface

no, but you can create one using mris_expand or simply sample halfway through the thickness of the cortex with --projfrac 0.5

cheers Bruce

On Thu, 19 Oct 2017, Nicholas Blauch wrote:

Hi Bruce,

That worked great. Thanks.

And for others reading, you might want to specify --surf pial in the call to mri_vol2surf, if your activations are expected in cortex. When I did it with no --surf specified, a face-selective localizer yielded weird results on the ventral surface. Specifying pial fixed it in this case. Maybe the average of white and pial would be optimal, or a weighted average if one is interested in different cortical layers? There is no mid-cortical surface by default, right?

best, Nick

  Message: 4
  Date: Wed, 18 Oct 2017 19:58:26 -0400 (EDT)
  From: Bruce Fischl <fischl@nmr.mgh.harvard.edu>
  Subject: Re: [Freesurfer] Registering T-maps to the inflated surface
  To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>
  Message-ID:
          <alpine.LRH.2.20.1710181957170.4903@gate.nmr.mgh.harvard.edu>
  Content-Type: text/plain; charset="utf-8"

  Hi Nick

  you only need to register once to all the surfaces. If you use spmregister
  to create a register.dat, you can then use mri_vol2surf with it and your T
  map t create a surface-based T map, which you should then be able to load
  as an overlay on top of any surface for that subject and hemi (e.g.
  lh.white, lh.inflated, lh.pial, lh.smoothwm, etc....)

  cheers
  Bruce


  On Wed, 18 Oct 2017, Nicholas Blauch wrote:

  > Hello to the folks at Freesurfer,
  >
  > I'm just getting started with your tools and am finding them very useful. Thanks for
  the great
  > work.?
  >
  > I am trying to register my functional images to freesurfer surfaces in order to
  overlay SPM T maps.
  > I have pre-processed and co-registered my functional images to the brain volume using
  SPM, where I
  > also ran functional analyses. I followed the instructions on the web for using
  spmregister. Doing
  > so?produces a register.dat file that seems to work well for overlaying my T maps onto
  the white,
  > orig, and pial surfaces, but not the inflated surfaces. When attempting to?register to
  the inflated
  > surface using tkregister, I get the error "ERROR: vertex 0 (14.6911,-132.739,-34.1424)
  is out of
  > range (113,162,-5)". When I attempt to overlay onto the inflated surface in
  freeview,?the locations
  > are not remotely correct (usually invisible, within the inflated surface).
  >
  > I think that freesurfer is basically doing a volumetric registration which is why it
  has trouble
  > with the inflated surface, which is mostly outside of the brain. Whereas I think the
  desired method
  > would be to?co-register a given functional/statistical volume to the freesurfer orig
  volume, and
  > then take advantage of links between orig and all surfaces created from it.?
  >
  > Does anybody know of a way to achieve this linking between an arbitrary volume and all
  surfaces? Or
  > of another workaround?to plot SPM T-maps on the subject's inflated surface??
  >
  > Thanks for any help.
  >
  > cheers
  > Nick
  >
  > --
  > Nicholas Blauch, B.S.
  > Lab Manager?
  > Computational Memory and Perception Laboratory
  > Department of Psychological and Brain Sciences
  > University of Massachusetts, Amherst
  >