Hi Chester
you can use the talairach.m3z to map to a common space (which is our nonlinear atlas space). The easiest thing is probably to do (e.g.)
mri_extract_label -t transforms/talairach.m3z aseg.mgz 17 lh.hippo.mgz
this will extract the lh hippo label and transform it into our common atlas space.
cheers Bruce
On Thu, 1 Oct 2015, Chester Dolph wrote:
Hello, 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.
Thanks, Chester
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