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), Christian Larsen (CL)

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 its indirect approach: alignment to a T1w 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.

There are many other estimation methods, a recent example, where a comparison to freesurfer eTIV is made, is:

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

Our 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

Upon completion of samseg, a txt file called sbTIV.log is produced which contains the sbTIV measures, plus other info on the structures that composed that measurement. An example of sbTIV.log is:

here be info

mri_segstats --sbTIVin <sbTIV.log> ...

When <sbTIV.log> is provided to mri_segstats, the sbTIV measure is read and added as 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 the Samseg-based segmentation. See surfer.nmr.mgh.harvard.edu/fswiki/sbTIV

and as found in aseg.stats:

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

Method

The Samseg-based segmentation data includes a labeling of all voxels inside the skull. This is in contrast to the older FreeSurfer .gca -based atlas, which was limited to brain structures of value. Samseg's labeling of intracranial voxels means that its ICV estimate in principle is immune to shrinking brain structures (where the .gca -based structures do not contain labels allowing immunity to this effect).

The method sums the following structures: TBD

Validation

The mri_sbTIV measure was validated against these reference sources:

dataset	description
SASHA	22 subjects, manual TIV from T2 scans
*'ADNI_T2	42 subjects, manual TIV from T2 scans
Buckner40	40 subjects, eTIV from FS v6.0, and SPM12
ADNI60	60 subjects, eTIV from FS v6.0, and SPM12
ADNI_714_1.5T	714 subjects, eTIV from FS v5.3
ADNI_1150_3T	1150 subjects, eTIV from FS v5.3
IXI_79	70 subjects, eTIV from FS v5.3, and SPM12

* as of March 2018, this data could not be found anywhere in the Martinos Center file system

The test subjects and scripts are located here: /cluster/fsm/users/samseg/<dataset>.

The SASHA dataset 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, and SPM12 eTIV from 179 subjects.

Project Notes

Tasks

NS - confirm Usage format and Validation plan with Contributors
CL - devise the sbTIV algorithm
AH - copy SASHA and ADNI_T2 datasets to samsseg/subjects dirs from locations shown in eTIV page
CL - run SPM12 eTIV function on Buckner40, ADNI60 and IXI_79
CL - create validation scripts, whereby given a set of sbTIV measures for a dataset, plot against the reference dataset (either manual values or eTIV) see Methods section of eTIV for details on SASHA scripts, and the Malone paper for their approach.
CL - create mri_sbTIV and update mri_segstats (per Usage statement above)

-Deletions are marked like this.
+Additions are marked like this.
 Line 21:
-{{{

mri_sbTIV ?

}}}

mri_sbTIV accepts ?????.  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>).
+Upon completion of samseg, a txt file called sbTIV.log is produced which contains the sbTIV measures, plus other info on the structures that composed that measurement.  An example of sbTIV.log is:
-Line 27:
+Line 24:
-mri_segstats ??? ...
+here be info
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+Line 28:
-When ??? 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:
+{{{

mri_segstats --sbTIVin <sbTIV.log> ...

}}}

When <sbTIV.log> is provided to mri_segstats, the sbTIV measure is read and added as an additional measure of brain volume to its output summary file.  From its help file:
-Line 32:
+Line 36:
-  based on a skull segmentation. See surfer.nmr.mgh.harvard.edu/fswiki/sbTIV
+  based on the Samseg-based segmentation. See surfer.nmr.mgh.harvard.edu/fswiki/sbTIV
-Line 36:
+Line 40:
-# Measure sbTotalIntracranialVolume, sbTIV, segmentation-based estimated Total Intracranial Volume, 1667606.252292, mm^3
+# Measure sbTotalIntracranialVolume, sbTIV, samseg-based estimated Total Intracranial Volume, 1667606.252292, mm^3
-Line 42:
+Line 46:
-description of method here
+The Samseg-based segmentation data includes a labeling of all voxels inside the skull.  This is in contrast to the older FreeSurfer .gca -based atlas, which was limited to brain structures of value.  Samseg's labeling of intracranial voxels means that its ICV estimate in principle is immune to shrinking brain structures (where the .gca -based structures do not contain labels allowing immunity to this effect).  



The method sums the following structures:  '''TBD'''
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+Line 56:
-||ADNI_T2||42 subjects, manual TIV from T2 scans||
+||'''*''''ADNI_T2||42 subjects, manual TIV from T2 scans||
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+Line 62:
+'''*''' as of March 2018, this data could not be found anywhere in the Martinos Center file system
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+Line 66:
-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, and SPM12 eTIV from 179 subjects.
+The SASHA dataset 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, and SPM12 eTIV from 179 subjects.