Alignment and Atlases

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-24-Standard SpacesWhy use a standard template space?• Compare across subjects and groups easily for every voxel in the brain• Standardize coordinates with others• Know where a voxel is automatically from an atlas• Mostly automated and no specific ROI drawing requiredWhy not use a standard template space?• Inconsistency among subjects• Inconsistency among groups – elderly versus younger• Use consistent anatomical ROIs with good anatomical knowledge• Lower threshold for multiple comparison adjustments
-25-• Hidden in GUI - right click on “DataDir” or set AFNI_ENABLE_MARKERS toYES in .AFNIRC• Manual Transformation proceeds in two stages:1. Alignment of AC-PC and I-S axes (to +acpc coordinates)2. Scaling to Talairach-Tournoux Atlas brain size (to +tlrc coordinates)• Stage 1: Alignment to +acpc coordinates: Anterior commissure (AC) and posterior commissure (PC) are aligned to be they-axisThe longitudinal (inter-hemispheric or mid-sagittal) fissure is aligned to be the yzplane,thus defining the z-axisThe axis perpendicular to these is the x-axis (right-left)Five markers that you must place using the [Define Markers] control panel:AC superior edgeAC posterior marginPC inferior edgeFirst mid-sag point = top middle of anterior commissure = rear middle of anterior commissure = bottom middle of posterior commissure = some point in the mid-sagittal planeAnother mid-sag point = some other point in the mid-sagittal planeThis procedure tries to follow the Atlas as precisely as possible➥Even at the cost of confusion to the user (e.g., you)
Page 4 and 5: -4-Alignment tools in AFNI (continu
Page 6 and 7: -6-• Most image registration meth
Page 8 and 9: -8-• AFNI program 3dvolreg is for
Page 11 and 12: -11-Motion correction - caveats•
Page 13 and 14: -13-align_epi_anat.py• Goal: Want
Page 15 and 16: -15-Alignment Visualization in AFNI
Page 17 and 18: -17-Rat BrainsAlignmentof12hourMang
Page 19 and 20: -19-ATLASES
Page 21 and 22: -21-ATLAS DEFINITIONSTemplate Space
Page 23: -23-Registration To Standard Spaces
Page 27 and 28: -27-• Stage 2: Scaling to Talaira
Page 29 and 30: -29-Automatic Talairach Transformat
Page 31 and 32: -31-Templates included with AFNITT_
Page 33 and 34: -33-Applying a transform to followe
Page 35 and 36: -35-@auto_tlrc Results are Comparab
Page 37 and 38: -37-Atlas/Template Spaces Differ In
Page 39 and 40: -39-From Space To SpaceTLRCMNIMNI-A
Page 41 and 42: -41-Atlases Distributed With AFNITT
Page 43 and 44: -43-Atlases Distributed With AFNI:A
Page 45 and 46: -45-[Where am I?]Shows you where yo
Page 47 and 48: -47-• whereami can report on the
Page 49 and 50: -49-The Future …• New atlases -
Page 51 and 52: -51-Neighborhoods in Space -Transfo
Page 53 and 54: -53-• Histogram cartoons:IIIJJJ
Page 55 and 56: -55-• grayscale underlay = J(x) =
Page 57 and 58: -57-• The future for 3dAllineate:
Page 59 and 60: -59-Appendix AInter-subject, inter-
Page 61 and 62: -61-• Anatomical coverage differs
Page 63 and 64: -63- Solutions to these problems:
Page 65 and 66: -65- Recipe above does not address
Page 67 and 68: -67-
Page 69 and 70: -69-Algorithmic Features• Goal is
Page 72 and 73: -72-Mutual Information• Entropy o
Page 74 and 75:
-74-Hellinger Metric• MI can be t
Page 76 and 77:
-76-3dAllineateʼs Symmetrical CR
Page 78 and 79:
-78-Test: Monkey EPI - Anat6 DOFHEL
Page 80 and 81:
-80-Test: Monkey EPI - Anat11 DOFHE
Page 82 and 83:
-82-• Listen up folks, IMPORTANT
Page 84 and 85:
-84- First goal is to mark top midd
Page 86 and 87:
-86-• AC-PC Markers Cheat Sheet T
Page 88 and 89:
-88-Notes on positioning AC/PC mark
Page 90 and 91:
-90-• Scaling to Talairach-Tourno
Page 92 and 93:
-92-Using the same methods as befor
Page 94 and 95:
-94-• Automatic creation of “fo
Page 96 and 97:
-96-“Warp on demand” viewing of
Page 98 and 99:
-98-• Class example - Writing ana
Page 100 and 101:
-100- Examination of time series fr
Page 102 and 103:
-102-Real-Time 3D Image Registratio
Page 104:
-104-• Screen capture fromexample
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Alignment and Atlases

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