Dictionary ========== .. list-table:: :widths: 1, 2, 6 :header-rows: 1 * - 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 `ITK-SNAP keyboard shortcuts `_ SABRE regions ------------- .. list-table:: :widths: 1, 2, 1, 3 :header-rows: 1 * - 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 -------------- .. list-table:: :widths: 1, 1, 5 :header-rows: 1 * - 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 --------------- .. list-table:: :widths: 1, 1, 5 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 1, 3 :header-rows: 1 * - 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 ^^^^^^^^^^^^^^^^^^^^ .. list-table:: :widths: 1, 3 :header-rows: 1 * - Acronym - Definition * - LSF - Left Sylvian Fissure * - LC - Left Central sulcus * - RSF - Right Sylvian Fissure * - RC - Right Central sulcus File names ---------- .. list-table:: :widths: 30, 70 :header-rows: 1 * - 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