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