• sbTIV

sbTIV - segmentation-based (estimated) Total Intracranial Volume

Contributors: Bruce Fischl (BF), Doug Greve (DG), Andrew Hoopes (AH), Oula Puonti (OP), Nick Schmansky (NS), Koen Van Leemput (KVL)

Total intracranial volume (TIV/ICV) is an important covariate for volumetric analyses of the brain and brain regions, where it can provide a proxy of brain volume. It is commonly used to correct for head size variation (ie. 'normalize' hippocampal volume size). The gold-standard method is manual delineation of T2 scans. Freesurfer provides its eTIV measure, described on this page, but the approach suffers from basing the estimate solely on aligned of a T1 scan to an atlas, and not by direct segmentation of skull.

• 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.

• Accurate automatic estimation of total intracranial volume: A nuisance variable with less nuisance Malone, et al. (2015) NeuroImage 104:366-372.

The segmentation-based estimate of total intracranial volume, sbTIV, attempts to provide the measure making use of the skull segmentation output by the Samseg processing stream. The freesurfer utilities mri_sbTIV and mri_segstats both provide this measure, where a skull segmentation volume is provided as input.

Usage

mri_sbTIV --i <skullsegvol> [--o <file>]

mri_sbTIV accepts a binary volume where 1 indicates skull and 0 is empty. It determines the TIV by insert brief description of algorithm here and outputs to stdout the estimate in mm3 (and optionally to the text file named by <file>). Note that mri_sbTIV development is based on a skull segmented by Samseg, but in principle could accept any skull segmentation volume.

mri_segstats --skullseg <skullsegvol> ...

When a skull segmentation is provided to mri_segstats, the same estimation provided by the algorithm underlying mri_sbTIV is used to insert an additional measure of brain volume to its output summary file. From its help file:

                5. sbTotalIntracranialVolume (sbTIV) - estimate of the intracranial volume
                based on a skull segmentation. See surfer.nmr.mgh.harvard.edu/fswiki/sbTIV

and as found in aseg.stats:

# Measure sbTotalIntracranialVolume, sbTIV, segmentation-based estimated Total Intracranial Volume, 1667606.252292, mm^3

Validation

The mri_sbTIV measure was validated against these reference sources:

The SASHA and ADNI_T2 datasets support the primary validation efforts, as this data is based on expert manual segmentations. The other datasets compare against the freesurfer eTIV of nearly 2000 subjects.

Project Notes

Tasks

• NS - confirm Usage format and Validation plan with Contributors
• AH,KVL,OP - generate skull_seg.mgz output from current T1-based Samseg stream

• AH - copy SASHA and ADNI_T2 datasets to samsseg/subjects dirs from locations shown in eTIV page

• AH - create validation scripts, whereby given a set of sbTIV measures for a dataset, plot against the reference dataset (either manual values or eTIV)
• AH,BF,DG - devise the sbTIV algorithm