External Email - Use Caution Hi Daniela,
On this page https://secure-web.cisco.com/1eUQpVvxrVeNEfeuknfSJu6n3plR5yKIy8iRlfATB5XV2S4Wq_68rpEnw4YyVZM9BjK4jMfItVUk3EBKG85JZGFeYB67XqxzUaW3sx_iQBKkuPpJnxHb70EvrWDP21B9zMFJAXpCVKvaAGxd2BG1YToPdu2TLDfqVo880z9p3OfdSus4qO0uJPBNy3Vb9DNri0QsNNhyuDL4_lqx9WtKk40t023R40UXi9hi5KGDYPp9HDW4NCQpoLsJFrL4ysUhX/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2FeTIV, it explains how Freesurfer estimates TIV. Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align an image with an atlas. The work demonstrates that a one-parameter scaling factor provides a reasonable TIV estimation (but biased). This method uses an atlas based spatial normalization procedure, and requires that the talairach.xfm be correct. Best, Yujing -----Original Message----- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Daniela Vecchio Sent: Wednesday, April 19, 2023 5:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] TIV from manually corrected aseg+aparc.mgz External Email - Use Caution Hi FreeSurfer Developers, For our study we had to manually correct some recon-all outputs due to some ROIs underestimation. For the purpose we manually edited the aparc+aseg.mgz file using the "voxel edit” command from Freeview. Then we use the mri_segstats command to extract volumes from the corrected aparc+aseg.mgz file. However, from the MRI_segstats we didn’t obtain a new TIV value. I want to ask if the TIV value is computed using the parcellation files (like aseg+aparc one) or instead using the brain.mgz file. How can I check that the TIV value reported in aseg.stats was unaffected from the underestimation we had to correct? Please find below the command we use to compute volumes from the corrected aseg+aparc file: mri_segstats --seed 1234 --seg /Applications/freesurfer/7.1.1/subjects/CorrectedSegmentations/${subj_id}.mgz --sum /Applications/freesurfer/7.1.1/subjects/${subj_id}/stats/AllVolumes.stats --pv /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --empty --brainmask /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/brainmask.mgz --brain-vol-from-seg --excludeid 0 --excl-ctxgmwm --supratent --subcortgray --in /Applications/freesurfer/7.1.1/subjects/${subj_id}/mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --surf-wm-vol --surf-ctx-vol --totalgray --euler --ctab /Applications/freesurfer/7.1.1/AreasList.txt --subject ${subj_id} Thank you for your support! Daniela _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1J4ZtXSfNXDI93pslVp-ho7wWHCLaVeMyN4HX8hQpkF-JQqNX5yNQ20tgCGH3dh86GwiQFUXBzN0DTDmgRYVPA7Czd9T2fO4jgr8rO4JiLxxOMrAGkxm7TQnJbDrhshZiUbaqAkiatCYzsaEPheBt3Qls2zl5mLLaGwBhX0rvtpRDQRyucy8JgHpHmtgDZpxmGmhPofzbpxBfl4N6AACprbjnFO7lx6tvb0SRfc3OTyt5eUKUKQ1JSh58Tfj6XOnI/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.
