Alignment and Atlases

More documents

Recommendations

Info

-82-• Listen up folks, IMPORTANT NOTE:Have you ever opened up the [Define Markers] panel, only to find the AC-PC markersmissing , like this:Gasp! Wheredid they go? There are a few reasons why this happens, but usually itʼs because youʼve made a copyof a dataset, and the AC-PC marker tags werenʼt created in the copy, resulting in theabove dilemma.➥ In other cases, this occurs when afni is launched without any datasets in thedirectory from which it was launched (oopsy, your mistake). If you do indeed have an AFNI dataset in your directory, but the markers are missingand you want them back, run 3drefit with the -markers options to create an emptyset of AC-PC markers. Problem solved!3drefit -markers
-83-• Class Example - Selecting the ac-pc markers: cd AFNI_data1/demo_tlrc ⇒ Descend into the demo_tlrc/ subdirectory afni & ⇒ This command launches the AFNI program➥ The “&” keeps the UNIX shell available in the background, so we can continuetyping in commands as needed, even if AFNI is running in the foreground Select dataset anat+orig from the [Switch Underlay] control panelPress IN to viewmarkers on brainvolumeThe AC-PCmarkersappear onlywhen the origview ishighlighted Select the [Define Markers]control panel to view the 5 markers forac-pc alignment Click the [See Markers] button to view the markers on the brainvolume as you select them Click the [Allow edits] button in the ac-pc GUI to begin markerselection
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 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
show all

Alignment and Atlases

You also want an ePaper? Increase the reach of your titles

Delete template?

Save as template?