Rewording to clarify in case the wording was confusing. What I would like to do is to use each registered ROI for intensity based analysis. I am confused how to use Freesurfer to register and align about three axis. I understand there is variability with positioning the head within the scanner of MRI. I am guessing one solution might be to align each ROI centroid to the same location. This seems to be a trivial concept, but I was hoping there was a simple way of doing this using Freesurfer tools. I appreciate your time and help.

On Sep 11, 2015, at 5:31 PM, CHESTER DOLPH <cdolp001@odu.edu> wrote:

Dear experts,

I look like to register a set of extracted hippocampus to a common atlas. Here is my workflow:

I used mri_binarize to get a mask of the hippocampus from aseg.mgz and then used mri_mask to mask the norm.mgz to get a volume of intensities. After this process, I noticed that hippocampus do not seem aligned in terms of the axial axis.

I have been looking at the registration tools at:

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferCommandsRegistration

Would someone please make a recommendation of a freesurfer tool well suited to registering a set of extracted left or right hippocampus to a common atlas? Also is there a flag to indicate the region, for instance from the look up table: $FREESURFER_HOME/FreeSurferColorLUT.txt

Thanks,
Chester