Re: [Freesurfer] Registering a parcellation from MNI_2mm space to subject native spac

you should use the method I posted

On 10/15/2014 04:42 PM, Marcelo Mattar wrote:

Hi Bruce,

Thanks for your response. A couple of follow-ups:

1. Is using bbregister usually better than using FLIRT? After all,

isn't it simply an affine transformation? 2) If I want to move my parcellation from MNI_2mm space to subject native space, shoud I use the MNI_2mm template as my input/movable volume and my SubjID as my subject? 3) What about cvs_register? Will I get a better registration outcome if I use this as opposed to bbregister, followed by mri_vol2vol?

Thank you very much, Bruce!

-- Marcelo

On Sat, Oct 11, 2014 at 5:04 PM, Bruce Fischl <fischl@nmr.mgh.harvard.edu mailto:fischl@nmr.mgh.harvard.edu> wrote:

Hi Marcelo

you can use bbregister to register the surfaces to another volume, and
mri_vol2surf to then map the volume onto the surface (or
mri_vol2vol to
apply the volume transform)

cheers
Bruce
On Sat, 11 Oct 2014, Marcelo Mattar wrote:

> Hello,
> I'm new to Freesurfer, and I'm lost in something that I believe
is very
> basic. I have a parcellation of the brain in .nii format that is
currently
> in MNI space (2mm). I would like to move this parcellation to
subject native
> space, so that I can extract the BOLD timeseries from each
region of the
> parcellation.
>
> I understand that an option I have is to simply use FSL tools
such as FLIRT
> or FNIRT and move the parcellation file to subject space (using
nearest
> neighbor interpolation). However, given that I have
reconstructed the
> subject's anatomy to the surface space, I believe I can do a
better job that
> just an affine transformation.
>
> What should I do in this case?
>
> 1) Is there any freesurfer tool that would allow me to register
a volume to
> another volume, but aided by surface information?
> 2) If so, what steps should I follow to extract BOLD timeseries
for each
> subject from the parcellation regions?
>
> Thank you very much,
>
> --
> Marcelo Mattar
> University of Pennsylvania
>
>
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu>
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer


The information in this e-mail is intended only for the person to
whom it is
addressed. If you believe this e-mail was sent to you in error and
the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to
you in error
but does not contain patient information, please contact the
sender and properly
dispose of the e-mail.

--

Marcelo Mattar http://about.me/marcelomattar

http://about.me/marcelomattar?promo=email_sig

---

Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer