Thank you so much for your really quick response, Nick! I just did it following your advice. However, I found AFNI can not read the result (".gii"). Actually, my main aim is do a cortical thickness analysis in a ROI. I just went over the old mails and found one person have same quesiton to me. One freesurfer expert answered this question and said use mri_surf2vol. I read the manual of mri_surf2vol very carefully. However, there are still not very clealy idea to me because the options of mri_surf2vol are a little complex. Now, what I have: 1. ROI mask: abc.nii. In this mask, the voxel value is 1 in the ROI and 0 out of the ROI. Most of this ROI is located in Gray matter and in Talarich Space. It is from my functional result and made by AFNI. I'm a very beginner to Free Surfer but I used AFNI more than 7 years. I perfer to use AFNI to analyze my functional data. My hypothesis is there are some anatomical differences (e.g., cortical thickness) in this ROI between groups. 2. There are twenty participants T1 data. All of them have been analyzed by "recon-all -autorecon-all".Therefore, each one has its own folder.
Could you please do me a favor and give me some detail advice to do it?
One potential way is transfer the thickness data into volume. Therefore, for each voxel in gray matter, I can know the thickness value. After getting this data I can dIs it possible?
Thanks, again!
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug Abuse - IRP
Biomedical Research Center
251 Bayview Blvd.
Suite 200 (NIDA)
Baltimore MD
21224
Tel: 443-740-2619
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Friday, November 14, 2008 2:38 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] for cortical thickness
Xiaochu,
You can convert the thickness data to ascii format like this:
mris_convert -c lh.thickness lh.white lh.thickness.asc
where the row data in the .asc file will be vertex_nun, x, y, z, thickness(mm)
You can convert to Gifti format, which is a new surface data file format for use in the freesurfer, nifti, afni, spm, brain voyager and caret community, like this:
mris_convert -c lh.thickness lh.white lh.thickness.gii
Nick
On Fri, 2008-11-14 at 14:05 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote:
Hi FreeSurfer Expert, Can I transfer the thickness data into other form, for example, Nifti,
AFNI or SPM? Thanks a lot!
Xiaochu Zhang PhD
Visiting Research Fellow
Neuroimaging Research Branch
National Institute on Drug Abuse - IRP
Biomedical Research Center
251 Bayview Blvd.
Suite 200 (NIDA)
Baltimore MD
21224
Tel: 443-740-2619
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