Alignment and Atlases

More documents

Recommendations

Info

-86-• AC-PC Markers Cheat Sheet The AC-PC markers may take some time for the novice to master, so in the interest oftime, we provide you with a little guide or “cheat sheet” to help you place markers on thisexample volume: i j k to: AC Superior Edge: 126 107 63AC Posterior Margin:127 108 63 PC Inferior Edge: 152 109 63 1st Mid-Sagittal Point: 110 59 60 2nd Mid-Sagittal Point: 172 63 60AC-PCmarkersmid-sagittalmarkers
-87- Once all 5 markers have been set, the [Quality?] Button is ready➥ You canʼt [Transform Data] until [Quality?] Check is passed➥ In this case, quality check makes sure two planes from AC-PC line to midsagittalpoints are within 2 o➭ Sample below shows a 2.43 o deviation between planes ⇒ ERRORmessage indicates we must move one of the points a little➭ Sample below shows a deviation between planes at less than 2 o . Qualitycheck is passed• We can now save the marker locations into the dataset header
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 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 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
show all

Alignment and Atlases

Create successful ePaper yourself

Delete template?

Save as template?