run_T1_sienax.sh — Brain Volume Estimation¶

Location: BRC_structural_pipeline/scripts/run_T1_sienax.sh
Authors: Ali-Reza Mohammadi-Nejad, Stamatios N Sotiropoulos
Last updated: 16 Mar 2021

Note

This script is called automatically by run_T1_preprocessing.sh when --regtype is 2 or 3. It does not need to be run manually.

Purpose¶

Implements a SIENAX-style brain volume estimation pipeline using FSL tools. It computes a skull-constrained volumetric scaling factor (vscale) by registering the T1 skull surface to MNI, then uses this factor to produce normalised brain volume estimates from the FAST partial volume estimates.

Processing Steps¶

1. Skull Surface Extraction¶

bet T1 SIENAX/T1_brain -s

The -s flag extracts the skull surface (T1_brain_skull) used for pairreg.

2. Skull-Constrained Registration¶

pairreg \
    MNI152_T1_2mm_brain \
    T1_brain \
    MNI152_T1_2mm_skull \
    SIENAX/T1_brain_skull \
    SIENAX/T1_to_MNI_linear.mat

Registers brain+skull simultaneously to MNI to get a skull-constrained affine.

3. Volume Scaling Factor¶

avscale SIENAX/T1_to_MNI_linear.mat MNI152_T1_2mm

Extracts x, y, z scale factors from the affine decomposition. The volumetric scaling factor is:

vscale = xscale × yscale × zscale

4. Tissue Volumes¶

For each tissue, the script computes:

unnormalised volume = mean(PVE) × voxel_count
normalised volume   = unnormalised × vscale

Tissues reported in report.sienax:

Label	Source PVE	Region
`pgrey`	`T1_brain_pve_1`	Peripheral grey matter (masked to periph. grey region)
`vcsf`	`T1_brain_pve_0`	Ventricular CSF (masked to ventricle region)
`GREY`	`T1_brain_pve_1`	Total grey matter
`WHITE`	`T1_brain_pve_2`	Total white matter
`BRAIN`	GM + WM	Total brain

Peripheral grey and ventricular masks are warped from MNI to native space using the inverse non-linear warp.

Parameters¶

Parameter	Type	Description
`--workingdir`	Path	T1 temp folder (provides `T1`, `T1_brain`, `reg/T1_to_MNI_nonlin_coeff_inv`)
`--sienaxtempfolder`	Path	Directory where all SIENAX intermediate and output files are written
`--fastfolder`	Path	FAST output folder (provides `T1_brain_pve_{0,1,2}`)
`--logfile`	Path	Log file path

Key Outputs¶

File	Description
`SIENAX/report.sienax`	Text report with `VSCALING`, `pgrey`, `vcsf`, `GREY`, `WHITE`, `BRAIN` volumes in mm³
`SIENAX/T1_to_MNI_linear.mat`	Skull-constrained registration affine
`SIENAX/T1_to_MNI_linear_avscale`	Full `avscale` output (contains scale factors)

Example report.sienax¶

VSCALING 1.0342
tissue             volume    unnormalised-volume
pgrey              453221.23 438375.81 (peripheral grey)
vcsf               12042.11  11644.50 (ventricular CSF)
GREY               672384.12 650191.33
WHITE              498221.44 481738.20
BRAIN              1170605.56 1131929.53