Alignment and Atlases

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-18-afni_proc.py – alignment h<strong>and</strong>ling • Single script to do all the processing of a typical fMRI pipeline including motioncorrection (3dvolreg), alignment (align_epi_anat.py)• combines transformations when possible• from example 6 in afni_proc.pyʼs prodigious help:afni_proc.py -subj_id sb23.e6.align \-dsets sb23/epi_r??+orig.HEAD \-do_block align tlrc \-copy_anat sb23/sb23_mpra+orig \-tcat_remove_first_trs 3 \-volreg_align_to last \-volreg_align_e2a \-volreg_tlrc_warp \…To process in orig space, remove -volreg_tlrc_warp.To apply manual tlrc transformation, use -volreg_tlrc_adwarp.To process as anat aligned to EPI, remove -volreg_align_e2a.
-19-ATLASES
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: -17-Rat BrainsAlignmentof12hourMang
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 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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