Alignment and Atlases

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-88-Notes on positioning AC/PC markers:➥➥The structures dimensions are on the order of typical high-res images. Do not fret about amatter such as: ➭ Q: Do I put the Sup. AC marker on the top voxel where I see still the the structure or onthe one above it?• A: Either option is OK, just be consistent. The same goes for setting the boundingbox around the brain discussed ahead. Remember, intra-subject anatomicalvariability is more than the 1 or 2 mm you are concerned about.Typically, all three markers fall in the same mid-saggital planeWhy, oh why, two mid-saggital points?➥➥[Quality?] Contrary to our desires, no two hemispheres in their natural setting can beperfectly separated by a mid-saggital plane. When you select a mid-saggital point, you aredefining a plane (with AC/PC points) that forms an acceptable separation between left andright sides of the brain. To get a better approximation of the mid-saggital plane, AFNI insists on another midsaggitalpoint and uses the average of the two planes. It also insists that these two planesare not off from one another by more than 2 o I am Quality! How do I escape the tyranny of the [Quality?] check?➥ If you know what you're doing and want to elide the tests:➭➭Set AFNI_MARKERS_NOQUAL environment variable to YES This is a times needed when you are applying the transform to brains of children ormonkeys which differ markedly in size from mature human brains.
-89- When [Transform Data] is available, pressing it will close the[Define Markers] panel, write marker locations into the dataset header, andcreate the +acpc datasets that follow from this one➥ The [AC-PC Aligned] coordinate system is now enabled in the mainAFNI controller window➥ In the future, you could re-edit the markers, if desired, then re-transform thedataset (but you wouldnʼt make a mistake, would you?)➥ If you donʼt want to save edited markers to the dataset header, you mustquit AFNI without pressing [Transform Data] or [Define Markers] ls ⇒ The newly created ac-pc dataset, anat+acpc.HEAD, is located in ourdemo_tlrc/ directory At this point, only the header file exists, which can be viewed when selectingthe [AC-PC Aligned] button ➥ more on how to create the accompanying .BRIK file later…
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-4-Alignment tools in AFNI (continu
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-6-• Most image registration meth
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-8-• AFNI program 3dvolreg is for
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-11-Motion correction - caveats•
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-13-align_epi_anat.py• Goal: Want
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-15-Alignment Visualization in AFNI
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-17-Rat BrainsAlignmentof12hourMang
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-19-ATLASES
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-21-ATLAS DEFINITIONSTemplate Space
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-23-Registration To Standard Spaces
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-25-• Hidden in GUI - right click
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-27-• Stage 2: Scaling to Talaira
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-29-Automatic Talairach Transformat
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-31-Templates included with AFNITT_
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-33-Applying a transform to followe
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-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
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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 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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