eTIV - Estimated Total Intracranial Volume
The estimated total intracranial volume calculation is based on this work:
[attachment:buckner2004.pdf A unified approach for morphometric and functional data analysis in young, old, and demented adults using automated atlas-based head size normalization: reliability and validation against manual measurement of total intracranial volume] Buckner et al. (2004) NeuroImage 23:724-738.
Basically, total intracranial volume is found to correlate with the determinant of the transform matrix used to align an image with an atlas. A one-parameter scaling factor results from this.
The Freesurfer binary that calculates eTIV is called mri_label_volume. It requires as input the subjects:
- transform matrix (talairach_with_skull.lta) which aligns with the atlas RB_all_withskull_2006-02-15.gca
- the Aseg volume (aseg.mgz)
Both of these are created by the standard recon-all stream (during -autorecon1 and -autorecon2).
Once those files are available, the command-line to issue is:
mri_label_volume -eTIV \ $sdir/transforms/talairach_with_skull.lta \ $sdir/aseg.mgz 17 53
where $sdir is the path to the subject's mri directory (ie, $SUBJECTS_DIR/<subjid>/mri). The '17' and '53' are label ID's, in this case left and right hippocampus (see the subjects /stats/aseg.stats file for IDs). The output will look like:
using eTIV from atlas transform of 1528 cm^3 processing label 17... 3822 voxels (3822.0 mm^3) in label 17, %0.250119 of eTIV volume (1528075) processing label 53... 4410 voxels (4410.0 mm^3) in label 53, %0.288598 of eTIV volume (1528075)