Alignment and Atlases

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-30- Templates in @auto_tlrc that the user can choose from:➥ TT_N27+tlrc: ➭ AKA “Colin brain”. One subject (Colin) scanned 27 times <strong>and</strong> averaged.(www.loni.ucla.edu, www.bic.mni.mcgill.ca) ➭ Has a full set of FreeSurfer (surfer.nmr.mgh.harvard.edu) surface models thatcan be used in SUMA (link). ➭ Is the template for cytoarchitectonic atlases (www.fz-juelich.de/ime/spm_anatomy_toolbox)• For improved alignment with cytoarchitectonic atlases, I recommend using the TT_N27template because the atlases were created for it. In the future, we might provideatlases registered to other templates.➥ TT_icbm452+tlrc: ➭ International Consortium for Brain Mapping template, average volume of452 normal brains. (www.loni.ucla.edu, www.bic.mni.mcgill.ca)➥ TT_avg152T1+tlrc: ➭ Montreal Neurological Institute (www.bic.mni.mcgill.ca) template, averagevolume of 152 normal brains. ➥ TT_EPI+tlrc:➭ EPI template from spm2, masked as TT_avg152T1. TT_avg152 <strong>and</strong> TT_EPIvolumes are based on those in SPM's distribution. (www.fil.ion.ucl.ac.uk/spm/)
-31-Templates included with AFNITT_N27TT_avg152T1TT_avg152T2TT_ICBM452 TT_EPI MNI_avg152T2
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: -29-Automatic Talairach Transformat
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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