i am trying to get fa value for left and right hippocampus.
i did brain region parcellation with freesurfer recon-all and get aparc+aseg.mgz file. then i made hippocampus mask based on it which has 256x256x256 dimensions. and i try to overlay my fa.mif (96x96x72) and get fa value of left and right hippocampus respectively but it did not work out. (said since both have different dimensions). i tried to mrresize but it did not work. are there any way that i can get fa value for only hippocampus?
You need to align both images, to be sure they are in the same space and then you can extract the values you are looking for. There are several options for doing this, but it depends on how have you processed your dMRI data, have you done EPI distortion correction? If so, you can use any software you want to do a linear registration, if not, you need to do a non-linear registration which complicates things a little bit.
thanks! i will let you know how it went:)