External Email - Use Caution I'm not sure what you are trying to do exactly. It looks like you want to get cortical volumes of regions in BN_Atlas. Please elaborate.
On 4/20/2023 12:52 AM, Garrett Tan wrote: > 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://secure-web.cisco.com/1oMUz5rWm_HCv-uOYBrdvd9i4rv5o-VvNqBEW9YMAhjFRppBS09tUHIWGNTEyecTNYIjDOYXSa4Umrx_dW5EQ1hwJWq7g_j4XwZeve8xzpKVaAdBIxMNBzPgHeKoDwM7uIy6XBQtICiXgA3OVcGBukSRsd7UPi2C21iSkcYwWTggTtyYxmsc540JdoxtajC9pQtG6a9uIpLm6yd0CxpT7xAo_svCGKV0XJaRBLbEE_feDFDd5xdpdPD7KHZ1cedd9AofXWGqTpb1DXnTgh0ZFXw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer _______________________________________________ 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.
