eTIV - Estimated Total Intracranial Volume


The estimated total intracranial volume calculation is based on this work:

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:

  1. transform matrix (talairach_with_skull.lta) which aligns with the atlas RB_all_withskull_2006-02-15.gca
  2. 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)

Checking validity