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

History of AFNI updates  

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August 09, 2022 10:36AM
Hi, Emily-

Re: <<I would like Z scores between 1.5 and 4 to be marked as "1s" and Z scores between -1.5 and -4 to be marked as "1s". The rest will be "0s" when binarizing.>>
Yes, you can do that like this:
3dcalc \
   -a DSET_STAT \
   -expr 'within(a,-4, -1.5) +within(a,1.5, 4)' \
   -prefix DSET_ROI_MASK

Re. calculating Dice in AFNI: Yes, there are a few options:
+ There are "3ddot -dodice ..."
+ 3dMatch has a Dice calculation (as well as a continuous-variable calculation, which might actually be of additional use/information here?); the Dice value would be in the 4th column of the output *.vals file
+ There is a fun, slice-wise Dice calculator, called 3dSliceNDice: 3dSliceNDice. That is generally more useful for calculating an interesting Dice comparison between larger ROI regions (like comparing masks).

... but also, there might be good ways to do a non-binarized comparison---those are often more informative, less sensitive to thresholding (which is arbitary, even if it happens to fall on a round-ish number), and use data more effectively. Visualizing the data together with translucent thresholding (such as used in the afni_proc.py QC stats images) is really quite helpful. In the AFNI GUI, that is done by apply the "A" and "B" buttons, and in @chauffeur_afni, you can do the same thing, such as shown here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/tutorials/auto_image/auto_%40chauffeur_afni.html#ex-5-overlay-beta-coefs-and-threshold-translucently-with-stats
with these opts:
-olay_alpha       Yes                                             \
    -olay_boxed       Yes                                             \

--pt
Subject Author Posted

thresholding and binarizing images

ebelleau August 09, 2022 09:47AM

Re: thresholding and binarizing images

ptaylor August 09, 2022 10:36AM

Re: thresholding and binarizing images

ptaylor August 09, 2022 10:44AM

Re: thresholding and binarizing images

Daniel Glen August 09, 2022 10:45AM

Re: thresholding and binarizing images

ptaylor August 09, 2022 10:50AM

Re: thresholding and binarizing images

ebelleau August 11, 2022 10:37AM