Hi Doug, thanks for the quick reply. I've been playing around with the commands you suggested and managed to get what seemed like a good registration by inspecting the green lines in tkregister.
However, I wasn't actually sure if I put the correct input:
bbregister --s colin --mov colin_tlrc_1x1x1.nii --reg ~/Documents/Analysis/eigenmodes/rsn_smith09/colin_register.dat --t1 --init-header
after the '--mov' option should i be using the anatomical template or the .nii file containing the 20 ICA components (4D)? I tried both (changing the between the --t1 and --bold options) and the anatomical template came out much better, but I thought the movable (--mov) is meant to be the functional image?
Also, wrt to mri_vol2surf, what should the --src_type, --projfrac options be set to in my case?
Also for --out_type, if I want an easy format to port to matlab?
Thanks!
> Date: Mon, 3 Mar 2014 14:20:55 -0500
> From: greve@nmr.mgh.harvard.edu
> To: freesurfer@nmr.mgh.harvard.edu
> Subject: Re: [Freesurfer] Resting State Networks on Cortical Surface
>
>
> you will need to create a registration between your volume (maps) and
> the anatomical. You can do this with bbregister. Then use mri_vol2surf
> to map your ICs to the surface
> doug
>
>
> On 03/02/2014 04:21 AM, Xuelong Zhao wrote:
> >
> > Hi,
> >
> > I am trying to display the 20 ICA components in this nifti file
> >
> > http://brainmap.org/icns/maps.zip
> >
> > onto anatomical template they've provided here
> >
> > http://brainmap.org/icns/colin_tlrc_1x1x1.nii
> >
> > My question is:
> >
> > How do I extract only the cortical surface from the anatomical
> > template and overlay
> > it with only parts of each ICA component that intersects with the surface?
> >
> >
> > Thanks!
> >
> >
> >
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>
> --
> Douglas N. Greve, Ph.D.
> MGH-NMR Center
> greve@nmr.mgh.harvard.edu
> Phone Number: 617-724-2358
> Fax: 617-726-7422
>
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