On 10/25/2012 04:25 PM, Shigetoshi Takaya wrote: > Dear Freesurfer experts, > > I would like to have your help. > > I have a volume data of a certain parameter on white/grey matter boundary > (X.nii). What I want to do are as follows: > Step 1: I want to register it onto a standard space using surface-based > alignment and smooth it. > Step 2: I want to generate the averaged images of several subjects on the > standard inflated surface. > > My questions are follows: > Q1) For Step 1, I guess I need to convert the image using mri_vol2surf > (X.nii --> X.mgh), then use mri_surf2surf and mris_smooth. If it is the case > what should I use for<target subject name> for mri_sur2surf? You should register X.nii to the anatomical with bbregister. This creates a registration file. Then use mri_vol2surf with this registration file to map to the surface. If you want the result to be on the individual subject's anatomy, then no need to specify a target subject. If you want it to be map from the individual's surface to the average surface, then specify fsaverage as the target. > > Q2) How to do Step 2? Do step 1 and specify fsaverage as the target (this puts them all in the same space). You can then put all of your subjects into one file with mri_concat. From there you can take the mean across all subjects to create a single map, or you can do something more sophisticated like fitting a GLM (mri_glmfit).
doug > > > Thanks in advance, > Shige > > _______________________________________________ > 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 gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html _______________________________________________ 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.
