AFNI Atlases – New framework and new features
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AFNI Atlases – New framework and new features Bringing the world to your data… New atlases standard (10 atlases are now default in AFNI) Desai Probability Maps, Eickhoff-Zilles, Talairach Daemon Subject-specific atlases from FreeSurfer Make or use atlases, templates, spaces for your subjects simply Elsevier’s BrainNavigator and BrainLink (in development) Saleem macaque atlas – MRI, histology (in development) Atlases, histology, journal citations for brain structures Where Am I? Atlas Colors Draw ROI Go to atlas location Daniel Glen, Ziad Saad, Richard Reynolds, Robert Cox Scientific and Statistical Computing Core, National Institute of Mental Health National Institutes of Health, Department of Health and Human Services, USA Use and modify ROIs from any atlas Treatment groups: pediatric, aged,... Animal support: rat, macaque, mouse,... AFNI atlas tools Desai DD MPM atlas shown Control the atlases, spaces, search radius to give as much information as you want Show ROIs from any atlas over your data Jump to an atlas location in your data MNI or Talairach space Choose one space or many spaces for output coordinates Do processing stream in TLRC/MNI/MNI_ANAT Atlases available to all spaces Neonatal brain template, Kazemi Karolinska rat template Scripting and Command line tools 3dclust -dxyz=1 -1clip 9.5 1 1000 func_FullF+tlrc > clusts.1D whereami -coord_file clusts.1D'[1,2,3]' -tab | less Automate processing and use atlas regions like other datasets 3dcalc \ -a 'func_data+tlrc' \ -b 'CA_EZ_ML::AMYGDALA' \ -expr 'a*step(b)' -prefix amy_active Link your data with a multitude of atlases, histology and on-line journal databases whereami -omask anat_roi+tlrc apply an atlas region to your data report on the overlap of ROIs with atlas-defined regions show where clusters fall in all available atlases
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Daniel Glen, Ziad Saad , Richard Reynolds, Robert Cox Scientific and Statistical Computing Core, National Institute of Mental Health National Institutes of Health, Department of Health and Human Services, USA. New atlases standard (10 atlases are now default in AFNI) - PowerPoint PPT Presentation
Transcript of AFNI Atlases – New framework and new features
AFNI Atlases – New framework and new features
Bringing the world to your data…
New atlases standard (10 atlases are now default in AFNI)Desai Probability Maps, Eickhoff-Zilles, Talairach Daemon
Subject-specific atlases from FreeSurfer
Make or use atlases, templates, spaces for your subjects simply
Elsevier’s BrainNavigator and BrainLink (in development)
Saleem macaque atlas – MRI, histology (in development)
Atlases, histology, journal citations for brain structures
Where Am I? Atlas Colors Draw ROI Go to atlas location
Daniel Glen, Ziad Saad, Richard Reynolds, Robert CoxScientific and Statistical Computing Core, National Institute of Mental Health
National Institutes of Health, Department of Health and Human Services, USA
Use and modify ROIs from any atlas
Treatment groups: pediatric, aged,...
Animal support: rat, macaque, mouse,...
AFNI atlas tools
Desai DD MPM atlas shown
Control the atlases, spaces, search radius to give as much information as you want
Show ROIs from any atlas over your data
Jump to an atlas location in your data
MNI or Talairach spaceChoose one space or many spaces for output coordinatesDo processing stream in TLRC/MNI/MNI_ANATAtlases available to all spaces
Neonatal brain template, Kazemi
Karolinska rat template
Scripting and Command line tools
3dclust -dxyz=1 -1clip 9.5 1 1000 func_FullF+tlrc > clusts.1Dwhereami -coord_file clusts.1D'[1,2,3]' -tab | less
Automate processing and use atlas regions like other datasets
3dcalc \ -a 'func_data+tlrc' \ -b 'CA_EZ_ML::AMYGDALA' \ -expr 'a*step(b)' -prefix amy_active
Link your data with a multitude of atlases, histology and on-line journal databases
whereami -omask anat_roi+tlrc
apply an atlas region to your data
report on the overlap of ROIs with atlas-defined regions
show where clusters fall in all available atlases
