Stage 8: Parcellate and lesion classification

../_images/stage8.png Stage summary: An individualized volumetric profile of regionalized tissue and lesion classes is generated.

SABRE regions

Region Lobe Name Acronym
3 Left Frontal L Superior Frontal LSF
4 Left Frontal L Middle Frontal LMF
5 Left Frontal L Inferior Frontal LIF
6 Left Frontal L Medial Inferior Frontal LMIF
7 Left Parietal L Superior Parietal LSP
8 Left Parietal L Inferior Parietal LIP
9 Left Occipital L Occipital LO
10 Left Temporal L Anterior Temporal LAT
11 Left Temporal L Posterior Temporal LPT
12 Left BG/Thal L Anterior BG/Thal LABGT
13 Left BG/Thal L Posterior BG/Thal LPBGT
14 Left Frontal L Medial Superior Frontal LMSF
15 Left Frontal L Medial Middle Frontal LMMF
16 Right Frontal R Superior Frontal RSF
17 Right Frontal R Middle Frontal RMF
18 Right Frontal R Inferior Frontal RIF
19 Right Frontal R Medial Inferior Frontal RMIF
20 Right Parietal R Superior Parietal RSP
21 Right Parietal R Inferior Parietal RIP
22 Right Occipital R Occipital RO
23 Right Temporal R Anterior Temporal RAT
24 Right Temporal R Posterior Temporal RPT
25 Right BG/Thal R Anterior BG/Thal RABGT
26 Right BG/Thal R Posterior BG/Thal RPBGT
27 Right Frontal R Medial Superior Frontal RMSF
28 Right Frontal R Medial Middle Frontal RMMF

Tissue classes

Label Name Acronym
3 Normal Appearing White Matter NAWM
4 Normal Appearing Grey Matter NAGM
5 sulcal CerebroSpinal Fluid sCSF
7 ventricular CerebroSpinal Fluid vCSF

Lesion classes

Label Name Acronym
1 deep white Subcortical Hyperintensities dwSH
2 deep white Black Holes dwBH
3 periventricular Subcortical Hyperintensities pvSH
4 periventricular Black Holes pvBH


Name Acronym Definition
Supra-Tentorial Total Intracranial Vault ST-TIV Sum of all classes (NAWM+NAGM+vCSF+sCSF+SH+BH)
Parenchyma   NAWM+NAGM+SH
Brain Parenchyma Fraction BPF Parenchyma/ST-TIV

Files and parameters

Input files

Filename Description
{session}_T1_IHC_inACPC_lobgrid.txt 2D landmarking grid file
{session}_T1_IHC_erode_inACPC_lobtrace.obj 3D landmarking file
{session}_FLEXedit FLEX lesion analysis file with manual intervention complete
{session}_LEedit Lesion Explorer (LE) lesion analysis file with manual intervention complete


Output files

{session}_SABREparcel_inACPC SABRE parcellation in ACPC space
{session}_SABREparcel SABRE parcellation in T1 native space
{session}_lesions FLEX and LE output; includes four lesion classes (pvSH, pvBH, dwSH, dwBH)
{session}_SABREseg Tissue class segmentation integrated with lesions
{session}_SABREseg_inACPC Tissue class segmentation integrated with lesions in ACPC space

Quality check

Filename Description
{session}_lesions Check that the 4 lesion classes have been correctly assigned
{session}_SABREparcel_inACPC Check that SABRE regions have been correctly applied in ACPC space
{session}_SABREparcel Check that SABRE regions have been correctly applied in T1 space