Label ID Scheme in BrainSuite

The description of labels in BrainSuite is given in XML files that are distributed in the atlas directories (BrainSuite18a/svreg/BCI-DNI_brain_atlas) in BrainSuite installation. These corresponding XML files are also copied to subject directories when we run the svreg sequence.

XML File: brainsuite_labeldescription.xml

This file contains description of surface and volume labels stored in *.nii and *.dfs files generated by BrainSuite/SVReg. The following files contain labels generated by SVREG.

Surface labels

subject.left.inner.cortex.svreg.dfs
subject.right.inner.cortex.svreg.dfs
subject.left.mid.cortex.svreg.dfs
subject.right.mid.cortex.svreg.dfs
subject.left.pial.cortex.svreg.dfs
subject.right.pial.cortex.svreg.dfs

Volume labels

subject.svreg.label.nii.gz
subject.svreg.init.label.nii.gz

The following files contains the sulcal/gyral region labels.

Surface labels

subject.left.mid.cortex.sulci.dfs
subject.right.mid.cortex.sulci.dfs
subject.left.smooth.mid.cortex.sulci.dfs
subject.right.smooth.mid.cortex.sulci.dfs

Volume labels

subject.sulci.label.nii.gz

The following file contains the tissue fraction labels
subject.pvc.label.nii.gz

Hierarchy

The label IDs are chosen in groups as described below:

0: background

subject.pvc.nii.gz (when 3 class classification is used).
1: CSF (cerebro-spinal fluid), 2: GM (gray matter), 3:WM (white matter), 4:CG (CSF/GM mixture), 5: GW (GM/WM mixture ), 6: CO (CSF/Other mixture)

Even: Right hemisphere
Odd: Left hemisphere

16-20: skull and scalp, brain labels

For BrainSuiteAtlas1

100-505: Cortical structures and hippocampus and amygdala.
600-900: Central, subcortical, cerebellum structures

For BCI-DNI and derivative atlases

In 3 digit label codes used in BrainSuiteAtlas1, the regions WM and GM parts of ROIs are combined, while in 4 digit label codes used in BCI-DNI and derivative atlases, WM and GM parts of ROIs have separate labels.
1XXX labels indicate Gray matter part of the ROI
2XXX labels indicate White matter part of the ROI

The labels are organized in the following hierarchy:

1100-1199: Frontal lobe regions (GM)
1200-1299: Parietal lobe regions (GM)
1300-1399: Temporal lobe regions (GM)
1400-1499: Occipital lobe (GM)

2100-2199: Frontal lobe regions (WM)
2200-2299: Parietal lobe regions (WM)
2300-2399: Temporal lobe regions (WM)
2400-2499: Occipial lobe (WM)

Sulcal and Gyral labels in *.sulc.* have IDs
4000 to 4071
Even: Right hemisphere sulci
Odd: Left hemisphere sulci

These correspond to the 36 sulci defined in the curves sulcal protocol defined in the sulcal_protocol_HD.xml file.

XML File: sulcal_protocol_HD.xml

This file contains the description of Sulcal Labels as described in the sulcal protocol. The protocol for tracing sulcal curve is included in this file. This file contains 36 curves that are an extension of the sulcal tracing protocol defined at Curve Protocol (26 curves).
Corresponding files
All DFC files including
Subject.left.mapped.dfc
Subject.right.mapped.dfc
Subject.left.mapped.refined.dfc
Subject.right.mapped.refined.dfc