Thanks Bruce and Doug! Follow-up questions: which anatomical volume does bbregister register the functional to? Also, is there any need to reorient the functional image before preprocessing?

On Tue, Sep 5, 2017 at 11:34 AM, Douglas N Greve <greve@nmr.mgh.harvard.edu> wrote:

On 08/31/2017 11:47 AM, Jiahe Zhang wrote:
> Dear Freesurfer experts,
>
> I have two questions regarding preproc-sess:
>
> 1) What is the default algorithm that does the functional-anatomical
> registration? And is there any way to change the default to other
> types of registration methods?
it uses bbregister. There is no easy way to change it
>
> 2) If I do not want to normalize to template, i.e. I want to keep the
> image in native space, should I be using -noreg or -noinorm?
Use the -per-session option and dont specify a hemisphere or mni305

>
> Thanks,
> Jiahe
>
>
> --
> Jiahe Zhang
> Ph.D. Candidate
> Department of Psychology
> Northeastern University
> 617-373-4789
>
>
> _______________________________________________
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

--
Douglas N. Greve, Ph.D.
MGH-NMR Center
greve@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422

Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

_______________________________________________
Freesurfer mailing list
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.

Jiahe Zhang

Ph.D. Candidate

Department of Psychology

Northeastern University

617-373-2649