Dictionary

Acronym	Name	Definition
SABRE	Semi-automatic Brain Region Extraction	A comprehensive semi-automatic pipeline that yields an individualized volumetric profile of regionalized tissue and lesion classes (see Dade et al., 2004)
LE	Lesion Explorer	Semi-automatic lesion analysis using PD/T2 (see Ramirez et al., 2011)
FLEX	Fluzzy Lesion EXtractor	Semi-automatic lesion analysis using FLAIR (see Gibson et al., 2010)
ST-TIV	Supra-Tentorial Total Intracranial Vault	Sum of all classes (NAWM+NAGM+vCSF+sCSF+SH+BH)
TIV-E	Total Intracranial Vault Extraction	Semi-automatic skull stripping process that provides an accurate measure of all sub-arachnoid parenchyma and CSF
	Parenchyma	NAWM+NAGM+SH
BPF	Brain Parenchyma Fraction	Parenchyma/ST-TIV

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SABRE regions

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

Tissue classes

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

Lesion classes

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

Landmarking

2D SABRE landmarking

Acronym	Definition
AC	Anterior Commissure
PC	Posterior Commissure
PE	Posterior Edge
CA	Central canal
M	Mid-sagittal plane
LPRON	Left PRe-Occipital Notch
RPRON	Right PRe-Occipital Notch
RSC	Right Superior Central sulcus
ROP	Right Occipito-Parietal sulcus
LSC	Left Superior Central sulcus
LOP	Left Occipito-Parietal sulcus

3D SABRE landmarking

Acronym	Definition
LSF	Left Sylvian Fissure
LC	Left Central sulcus
RSF	Right Sylvian Fissure
RC	Right Central sulcus

File names

Filename	Description
{session}_T1	T1 MRI in native space
{session}_PD	PD MRI in native space
{session}_T2	T2 MRI in native space
{session}_FL	FLAIR MRI in native space
{session}_PD_inT1_IHCpre	PD MRI coregistered and resliced to T1 acquisition space and corrected for inhomogeneity using N4 to create TIVauto mask (intermediate file)
{session}_T2_inT1_IHCpre	T2 MRI coregistered and resliced to T1 acquisition space and corrected for inhomogeneity using N4 to create TIVauto mask (intermediate file)
{session}_FL_inT1_IHCpre	FLAIR MRI coregistered and resliced to T1 acquisition space and corrected for inhomogeneity using N4 to create TIVauto mask (intermediate file)
{session}_PD_inT1_IHC	PD MRI in T1 space and corrected for inhomogeneity using N4
{session}_T2_inT1_IHC	T2 MRI in T1 space and corrected for inhomogeneity using N4
{session}_FL_inT1_IHC	FLAIR MRI in T1 space and corrected for inhomogeneity using N4
{session}_TIVauto	Total Intracranial Vault (TIV-E) mask
{session}_TIVedit	Total Intracranial Vault (TIV-E) mask with manual intervention
{session}_T1_IHCpre_iso	Isotropic T1
{session}_T1_IHCpre_toACPC.mat	T1-to-ACPC rotation matrix
{session}_T1_to_ACPC.air	T1-to-ACPC air file
{session}_ACPC_to_T1.air	ACPC-to-T1 air file
{session}_T1_IHC	T1 MRI with TIVedit mask N4 inhomogeneity correction
{session}_T1_IHC_TIV	Final inhomogeneity corrected T1 MRI with skull and non-brain tissue masked out using {session}_TIVedit
{session}_seg	Tissue segmentation in T1 acquisition space
{session}_seg_vcsf	Tissue segmentation with ventricles manually reassigned
{session}_seg_vcsf_st	Tissue segmentation with ventricles manually reassigned and subtentorial tissue removed leaving only TIV-supratentorial (st) voxels
{session}_T1_IHC_inACPC	T1 MRI aligned to the plane defined by the anterior and posterior commissure and resliced to isotropic voxels
{session}_T1_IHC_erode_inACPC	3D eroded T1 MRI in ACPC space
{session}_T1_IHC_erode	3D eroded T1 MRI in T1 native space
{session}_LEauto	Automatically generated LE lesion mask file
{session}_LEjux	Automatically generated LE lesion mask file (greater false positive rate), useful to inform decisions about juxtacortical or missed lesions
{session}_LEedit	LE lesion mask after manual intervention / quality check
{session}_FLEXauto	Automatically generated FLEX lesion mask file
{session}_FLEXedit	FLEX lesion mask after manual intervention / quality check
{session}_T1_IHC_inACPC_lobgrid.txt	2D landmarking grid file
{session}_T1_IHC_erode_inACPC_lobtrace.obj	3D landmarking file
{session}_T1_IHC_inACPC_parcelgrid.txt	2D landmarking grid file after transformation
{session}_T1_IHC_erode_inACPC_parcel.obj	3D landmarking file after transformation
{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