External Email - Use Caution Hi FreeSurfer Experts,
I am using Brainnetome Atlas in FreeSurfer to calculate the brain volume. The cortical regions are done smoothly by using mris_ca_label->mris_anatomical_stats with materials on https://secure-web.cisco.com/1p7TY1frW67uqViolqd97Sub3WUDGgPjPK0_YAEmmtEENBBjRqkxRhrM7lhQNbQoPTsnER7AEPASg0AMWvbh6ul9GG-VZIQL-qXWdva_lU2kvgeWbLOUKfHebFsSJi8SqqRlrWZCDXtotZtMgyb_wugL_-b6quUDqFpQbuKUrdh6fTEHlsGrK7IOqAVCheGDZi2YHdXybErdaYLFTq6vEoyF8XOTvbLUq_a_HWEiVy7Q6_Vy2TPb2tgjnMnSM5nNDLEAnuP2WUdlqvoKAyElf2GqlxaalTg_oxbGYfuT37Yaj9E0yuHwhq6samKGKSO-AbqTpoqjt5589vCtDhss-bQ/https%3A%2F%2Fatlas.brainnetome.org%2Fdownload.html However, when I was trying to get the volume of subcortical regions (the hippocampus, amygdala, thalamus, and basal ganglia), they are excluded since the ?h.cortex.label files do not include them. My plan was to use aseg.mgz to get each subcortical regions and do the same procedure as for the cortical regions. However, mri_ca_label did not allow me to create .annot from BN_Atlas_subcortex.gca from Brainnetome website. So I continued using mris_convert to convert .gca to label.mgz, and I am stuck here. Is there any way to get the subcortical regions’ .gcs file, or even an easier way to calculate the volume of subcortical regions in brainnetome atlas from FreeSurfer? Best, Garrett _______________________________________________ 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 Mass General Brigham Compliance HelpLine at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
