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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Daniel Glen
June 30, 2020 02:22PM
Some variants of these steps would work:

# set minimum and maximum values
set minthresh = 3.3
set maxthresh = 100

# which ROI to use
set roiindex = 4

# count thresholded values within mask region
3dBrickStat -count -non-zero -mask rois.niml.dset"<$roiindex>" stats.niml.dset"<$minthresh..$maxthresh>"

# or in two steps like this:
# First limit the number of vertices to the region with something like this
3dcalc -a rois.niml.dset -b stat.niml.dset -expr "equals(a,$roiindex)*b" -prefix maskedstat.niml.dset
# Count nodes in masked stats above threshold
3dmaskdump -noijk -mask maskedstats.niml.dset"<$minthresh..$maxthresh>" maskedstats.niml.dset | wc -l
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Subject Author Posted

vertices in a specific anatomical region above a given q threshold

amehta June 30, 2020 12:33AM

Re: vertices in a specific anatomical region above a given q threshold

Daniel Glen June 30, 2020 02:22PM