AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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Anonymous User
July 10, 2012 10:28AM
Thank you, it's somewhat inconvenient that this functionality isn't built into AFNI, but it's easy enough to composite in imagmagick. Here's an example of compositing two axial slices: 
# generate a black background
3dcalc -a anat.nii -expr 0 -prefix black_background.nii

# generate an image of the first functional layer (see AFNI driver README for more options)
afni -com "SWITCH_ANATOMY anat.nii" -com "SWITCH_OVERLAY layer1.nii" -com "SET_XHAIRS OFF" -com "SAVE_PNG axialimage layer1.png"

# generate an image of the second functional layer on a black background
afni -com "SWITCH_ANATOMY black_background.nii" -com "SWITCH_OVERLAY layer2.nii" -com "SET_XHAIRS OFF" -com "SAVE_PNG axialimage layer2.png"

# make the black (actually, #050505) background transparent
convert layer2.png -transparent '#050505' layer2.png

# generate the composite image
composite layer2.png layer1.png composite_image.png
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Subject Author Posted

stack multiple overlays in afni viewer

Anonymous User July 09, 2012 03:43PM

Re: stack multiple overlays in afni viewer

Isaac Schwabacher July 09, 2012 04:16PM

Re: stack multiple overlays in afni viewer

judd storrs July 09, 2012 05:02PM

Re: stack multiple overlays in afni viewer

Anonymous User July 10, 2012 10:28AM

Re: stack multiple overlays in afni viewer

Chad N July 10, 2012 10:54AM