Alignment and Atlases

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-70-Cost Functions• Except for least squares (actually, ls minimizes E = 1.0 – Pearson correlation coefficient), allcost functions are computed from 2D joint histogram of J(x) <strong>and</strong> I(T(x,w)) Start <strong>and</strong> final histograms can be saved using hidden option -savehistBeforeAfterSourceimageSource image= rotated copyof Base imageBase image
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 and 24: -23-Registration To Standard Spaces
Page 25 and 26: -25-• Hidden in GUI - right click
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: -69-Algorithmic Features• Goal is
Page 73 and 74: -73-Normalized MI• NMI = H({r ij
Page 75 and 76: -75-Correlation Ratio• Given 2 (n
Page 77 and 78: -77-Test: Monkey EPI - Anat6 DOFCRm
Page 79 and 80: -79-Test: Monkey EPI - Anat11 DOFCR
Page 81 and 82: -81-Appendix CTalairach Transform f
Page 83 and 84: -83-• Class Example - Selecting t
Page 85 and 86: -85- Second goal is to mark inferio
Page 87 and 88: -87- Once all 5 markers have been s
Page 89 and 90: -89- When [Transform Data] is avail
Page 91 and 92: -91-• Class example - Selecting t
Page 93 and 94: -93- Once the quality check is pass
Page 95 and 96: -95- How does AFNI actually create
Page 97 and 98: -97-Creating follower data• Writi
Page 99 and 100: -99-• Command line program adwarp
Page 101 and 102: -101-No longer discussed here, see
Page 103 and 104: -103-• Realtime motion correction
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