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
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
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Nicholas Blauch