Thank you so much for your response, Nick! I uploaded "ROI5.nii" (i.e., abc.nii) just now. This ROI has been in Talarich space. Actually, it is from my group functional data. So I did not have corresponding T1-data.
BTW: when can I read the web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask? I hope I can read it ASAP. If it is possible, could you please do me a favor and send the draft to me? 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:[EMAIL PROTECTED] Sent: Monday, November 17, 2008 12:59 PM To: Zhang, Xiaochu (NIH/NIDA) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] RE: for cortical thickness Xiaochu, I'm putting together a web page describing the steps taken to get cortical thickness from an ROI defined by a volume mask. Can you send me these two files so that I can make sure the steps work correctly? 1) the ROI mask file (what you are calling 'abc.nii') 2) the T1-weighted anatomical volume of the subject from which abc.nii was created. i need this file to register to a template volume. You can post those files (available only to me) by uploading to our file drop: https://www.nmr.mgh.harvard.edu/facility/filedrop/index.html Nick On Sat, 2008-11-15 at 00:48 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > Hi, FreeSurfer export, > > Thank you very much for response! > Now, under some export's help, I used to the mri_surf2vol to transfer cortex thickness into nifti. > The below line is what I used. > mri_surf2vol --surfval ../surf/lh.thickness --hemi lh --fillribbon > --template orig.mgz --volregidentity ${subid} --outvol lh.ribbon.nii > > I checked the result and found the voxel outside the gray matter is always zero and in the gray matter is about 0-3. Could you please do me a favor and tell me whether these data is cortex thickness or not? > If they are cortex thickness, why are they always different. In my mind, it should be same in one direction because we calculate the distance between the white matter line and the gray matter line. > > Thanks a lot! > All the best, > Xiaochu > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
