Re: [Freesurfer] illustration of a nifti volume on fsaverage

You can use mri_coreg to register the volume to fsaverage, then use the registration when running freeview or tksurfer

On 5/9/17 10:19 AM, james pardon wrote:

Thank you Bruce. What if the nifti volume has not been processed at all in Freesurfer? My only aim is to illustrate an overlay on FSAVERAGE, with the obvious caveat of skipping surface construction for this nifti.

Thanks, James

On Tue, May 9, 2017 at 2:42 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

if the nifti volume is from an individual subject that has been
run through recon-all (e.g. an fmri map):

1. Use bbregister to register the fmri to the recon surfaces
2. Use mri_volsurf to sample the fmri data onto the surface
3. Use mri_surf2surf to map from the individual to fsaverage

cheers
Bruce



On Tue, 9 May 2017, james pardon wrote:

    Dear All,
    Apologies in advance for the naive question. Could you please
     let me know
    what is the best way of transferring a nifti overlay volume to
    fsaverage,
    solely for illustration purposes? I think I should start by
    registering with
    fsaverage volume and then overlay with Freeview, but I'm not
    sure what tools
    from Freesurfer I should use for 1) between subject volume
    registration
    (nifti volume to fsaverage volume) 2) fsaverage volume to
    fsaverage surface.

    Thank you,
    James


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