Lab Manual:Publishing

Rendering Brains (2D)

Steps for rendering and dumping publication quality brain slices with Afni:

• Make your brain the right color
  • Don't get caught with washed out brains!
  • To do this click on the brain image in afni and drag the mouse diagonally across the brain. Play with this until the background looks black (not gray).

• Make the activation the right color
  • If you used the "openafni" command, then the threshold should already be set to the right color.
  • If not, make sure that your color bar marks the appropriate significance levels.

• Smooth your activation (maybe)
  • click on "Define Datamode"
  • click "Warp OLay on Demand" (in the middle of this panel)
  • Click the "Stat resam mode" menu and select "Cu". (for "cubic" ... you may need to also do this with "OLay resam mode")
  • If this ends up looking bad, don't use it after all.

• Get rid of dorky green cross hairs
  • If you want to keep the cross hairs, make them white.
    • On the far left in afni there is a option box called "Color". select white.
    • (note: cross hairs might not show up on high resolution brains.)
  • Or get rid of the crosshairs
    • On the far left in afni there is a option box called "Xhairs"...select none.

• Get high resolution brains
  • First find the slice you want to save. Afni will get very slow after the last step.
  • Click "Define Datamode" (if not already open)
  • Click "Warp ULay on Demand" (at the top of the panel)
  • Change Resam (mm) to either .5 (pretty good resolution) or .1 (really good resolution)

• Save to the right format
  • Click "Disp" in the bottom left corner of each brain window and select the right format (probably tiff or eps).
  • Click sav1.xxx in the bottom left corner of each brain window to save your slices to your current directory

Rendering brains (3D)

Steps for rendering and dumping publication quality volumes with Afni:

Illustrator cheat sheet

Here is a good reference for using illustrator:

Poster Template

Here is a poster template from 2008 (Author: Kacey Ballard). Here is another poster template from 2014 (Author: Charlene Wu).

Poster Printing

You can print posters in the printer room on the 3rd floor (rm 321) free of charge. You will need a keycard to enter the room (ask a lab member or Harry to get).

These instructions are for printing from the Mac in the poster printer room (highly recommended). Instructions are posted for using the PC (but there are sometimes issues in importing your ppt file into the Windows version of Powerpoint).

• My original document was a powerpoint file, single slide, landscape orientation, width = 56, height = 36.
• Go to File -> Page Setup, You can view your ppt dimensions here.
• Select 'Options'
• Click on the 'Format for' menu.
• Select 'poster-pr.stanford.edu'
• Click on the 'Paper Size' menu.
• Select '36x60'
• Make sure to scale at 100%
• Click OK in both 'Page Setup' Windows.
• Go to File->Print,
• Select 'poster-pr.stanford.edu' for the printer.
• Click on the drop down menu below 'Presets'
• Click on 'Paper Handling'
• Select the 'Scale to fit paper' box
• Click on the 'Destination Paper Size' menu
• Select '36x60'
• Click on the drop down menu below 'Presets'
• Click on 'Copies & Pages'
• Click on the 'Scale to Fit Paper' box
• Update the Preview by deselecting and selecting the 'Show Quick Preview' box
• Make sure that the preview looks appropriate

• • OPTIONAL: Adjust the print quality
  • Click on the drop down menu below 'Presets'
  • Click on 'Image Quality'
  • Click on 'Print Quality' and select 'Max Quality + Enhanced IQ.' Note that this print job will take the printer a while to process and print (20-25 minutes total).

• Click Print in the 'Copies & Pages' menu to send to the printer
• The printer will say receiving and display the percentage.