After generating a cortical surface rendering, I would like to overlay my EPI activation maps.
I considered rendering a cortical surface for all my participants but, they are all normalized to MNI space.
Despite the structural variabilities which remain even after normalization, is it still common for people to use a single FreeSurfer rendering for visualization (given all your EPI data are also normalized to MNI)?
-T
Hi Tim,
I'm not quite sure what you are asking. What do you mean by "single FreeSurfer rendering"? What are you using to analyze your functional data? If you've normalized your functional data to a template (eg, MNI305), you can still map the individual's functional to the individual's surface (as long as the normalization is linear). You simply need a freesurfer-style registration between your normalized functional and the freesurfer anatomical (eg, orig volume). You can do this manually with tkregister2 (run with --help). You can also use FSL's FLIRT to generate an initial matrix and then check it with tkregister2. We also have a program called fsl_rigid_register which is a FLIRT wrapper (run with -help to get docs).
doug
On Mon, 25 Jul 2005, Timothy O'Keefe wrote:
After generating a cortical surface rendering, I would like to overlay my EPI activation maps.
I considered rendering a cortical surface for all my participants but, they are all normalized to MNI space.
Despite the structural variabilities which remain even after normalization, is it still common for people to use a single FreeSurfer rendering for visualization (given all your EPI data are also normalized to MNI)?
-T
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
you definitely *don't* want to average your functional data in the 305 space then put it on a surface. You're much better off using our averaging tools and displaying it on an average surface.
cheers, Bruce On Mon, 25 Jul 2005, Doug Greve wrote:
Hi Tim,
I'm not quite sure what you are asking. What do you mean by "single FreeSurfer rendering"? What are you using to analyze your functional data? If you've normalized your functional data to a template (eg, MNI305), you can still map the individual's functional to the individual's surface (as long as the normalization is linear). You simply need a freesurfer-style registration between your normalized functional and the freesurfer anatomical (eg, orig volume). You can do this manually with tkregister2 (run with --help). You can also use FSL's FLIRT to generate an initial matrix and then check it with tkregister2. We also have a program called fsl_rigid_register which is a FLIRT wrapper (run with -help to get docs).
doug
On Mon, 25 Jul 2005, Timothy O'Keefe wrote:
After generating a cortical surface rendering, I would like to overlay my EPI activation maps.
I considered rendering a cortical surface for all my participants but, they are all normalized to MNI space.
Despite the structural variabilities which remain even after normalization, is it still common for people to use a single FreeSurfer rendering for visualization (given all your EPI data are also normalized to MNI)?
-T
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Doug Greve -
Timothy O'Keefe