AFNI & FMRI - the AFNI/NIfTI Server

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–39–AFNI at the NIH Scanners• AFNI can take images in “realtime” from an externalprogram and assemble them into 3D+time datasets slice-byslice•Jerzy Bodurka (FMRIF) has set up the GE Excite-basedscanners (3T-1, 1.5 T, NMRF 3 T, and 7 T) to start AFNIautomagically when scanning, and send reconstructedimages over as soon as they are available:! For immediate display (images and graphs of time series)! Plus graphs of estimate subject head movement• Goal is to let you see data as it is acquired, so that if thereare any big problems, you can fix them right away! Sample problem: someone typed in the imaging field-ofview(FOV) size wrong (240 cm instead of 24 cm), and gotgarbage data, but only realized this too late (aftersubject had left the scanner and gone home) — D’oh!–40–A Quick Overview of AFNI• Starting AFNI from the Unix command line! afni reads datasets from the current directory! afni dir1 dir2 … reads datasets from directories listed! afni -R reads datasets from current directory and from alldirectories below it• AFNI also reads a file named .afnirc from your home directory! Used to change many of the defaultso Window layout and image/graph viewing setup; popup hints; whether tocompress .BRIK files when writingo cf. file README.environment in the AFNI documentation• Also can read file .afni.startup_script to restore the windowlayout from a previous run! Created from Define Datamode->Misc->Save Layout menuo cf. file README.driver for what can be done with AFNI scripts
–41–AFNI controller window at startupCoordinates ofcurrent focus pointTitlebar shows current datasetsSwitch to differentcoordinate systemControl crosshairsappearanceTime indexOpen images andgraphs of datasetsOpen new AFNIcontrollerHelp ButtonClose this controllerMarkers controltransformation to+acpc and +tlrccoordinatesControls colorfunctional overlayMiscellaneous menusSwitch betweendirectories, underlay(anatomical) datasets,and overlay(functional) datasetsControls display ofoverlaid surfaces–42–AFNI Image ViewerDisp and Montcontrol panels
Page 5 and 6: -9-Precession of Magnetization M•
Page 7 and 8: -13-Material Induced Inhomogeneitie
Page 11 and 12: -21-Neurophysiological Changes & FM
Page 13 and 14: -25-• FMRI experiment designFMRI
Page 16 and 17: -31-Fundamental AFNI Concepts• Ba
Page 18 and 19: -35-AFNI Dataset Files - II• AFNI
Page 22 and 23: -43-AFNI Time Series Graph ViewerDa
Page 24 and 25: -47-• Batch mode programsOther Pa
Page 26 and 27: -51-SUMA Teaser MovieColor from AFN

AFNI & FMRI - the AFNI/NIfTI Server

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