1. Yes, recon-all is needed. We can read nifti and analyze, but please avoid using analyze if you can as it doesn't keep track of the direction cosines.
2. recon-all will run mris_register. You can run bbregister to register your anatomicals to your functionals.
3. You an run mri_vol2surf to sample onto the surface, then mri_surf2surf to transform into the common space. If you specify .mgz as the output format then MRIread.m or load_mgh.m will load them into matlab.
cheers Bruce On Mon, 15 Feb 2010, Joonkoo Park wrote:
Hi,
I'm completely new to FreeSurfer, and I'd like to get some guide to surface-based inter-subject registration in analyzing some fMRI data.
I have an anatomical image (e.g. t1-spgr or mprage) and functional images (e.g. epi) in NIFTI or ANALYZE format for each subject. In each subject's native space (typically using SPM), I perform some GLM and get some statistical parametric maps (SPMs) for each subject (note that the anatomical image and the resulting functional image are co-registered). Now, I'd like to use the surface-based normalization (or I realized that this procedure is called registration in the freesurfer community) procedure to normalize the anatomical and the functional images to a standard space. Could you please guide me what steps I need to perform in order to achieve this goal?
Here are some specific questions:
- What command shall I use to get the nifti/analyze images into the
freesurfer format? I was wondering if recon-all is really necessary. I heard that it takes more than a day to do one subject, and I don't think I need all those results for my purpose.
- I found that the command "mris_register" will give me what I want
at least for the anatomical data. But how do I do the same for the functionals? Also, how will I make sure that my anatomicals and functionals are co-registered?
- I need to be able to get into the data structure after
inter-subject normalization. For the nifti/analyze files, there's an SPM command that will bring all the data into a matrix in Matlab. But for the freesurfer format, is there a way to import the surface-based files into Matlab so that I can play with the output data?
I may not be asking in the right order or even in the right way. But I'm thinking that any FreeSurfer guru should be able to help me. I searched through the archive and the documentations but wasn't satisfactory.
Thanks in advance!
Joon
-- Joonkoo Park Ph.D. Candidate, Cognition & Cognitive Neuroscience Department of Psychology, University of Michigan _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer