Stage 8: Parcellate and lesion classification¶
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Stage summary: An individualized volumetric profile of regionalized tissue and lesion classes is generated. |
SABRE regions¶
| Region | Lobe | Name | Acronym |
|---|---|---|---|
| 1 | Left Temporal | L Hippocampus | LSBHV |
| 2 | Right Temporal | R Hippocampus | RSBHV |
| 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 Matter Hyperintensities | dWMH |
| 2 | deep Lacunes | dLACN |
| 3 | periventricular White Matter Hyperintensities | pWMH |
| 4 | periventricular Lacunes | pLACN |
| 6 | Perivascular Spaces | PVS |
Volumes¶
| 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 |
Parameters¶
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 |