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 <cdolp...@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
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