Zhang, The web page describing the steps to extract cortical thickness data for your volume-space defined ROI is found here:
https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness Nick On Mon, 2008-11-17 at 14:02 -0500, Zhang, Xiaochu (NIH/NIDA) [F] wrote: > 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
