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
_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
