Stage 8: Parcellate and lesion classification
========================

+----------------------+---------------------------------------------------------------------------------------------+
|.. image:: stage8.png | **Stage summary:** An individualized volumetric profile of regionalized tissue and lesion   |
|                      | classes is generated.							                     |
+----------------------+---------------------------------------------------------------------------------------------+

SABRE regions
-------------
 
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   * - 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
--------------

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   * - 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
---------------
     
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   * - 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   
     
Volumes
--------

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   * - 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
^^^^^^^^^^^

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   * - 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
^^^^^^^^^^^^

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   * - ``{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
--------------

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   * - 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