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  

Previous Message Next Message
Message List New Topic Print View
|
Daniel Glen
September 10, 2021 12:15PM
This particular use of 3dLocalstat may not be what you expect. The stat parameter here essentially computes a voxel value based on the bin step. Consider this example:

3dLocalstat -prefix testperc.nii.gz -nbhd 'SPHERE(-5)' -stat 'perc:1:100:25' func_slim+tlrc.'[1]'

The stat format for the percentile uses "perc:start:stop:step" as its parameters all expressed in percent (not decimal fractions). This command computes the values at the 1%, 26%, 51% and 76%ile in a 5mm radius local neighborhood around each voxel. The output has 4 subbrick volumes. Switch among these with the Overlay panel control.

The median would be computed with either of these commands, and either would have only a single output subbrick volume (the start and stop are equal):

3dLocalstat -prefix testperc2.nii.gz -nbhd 'SPHERE(-5)' -stat 'perc:1:100:25' func_slim+tlrc.'[1]'
3dLocalstat -prefix test_median.nii.gz -nbhd 'SPHERE(-5)' -stat 'median' func_slim+tlrc.'[1]'
Reply Quote
RSS
Subject Author Posted

3dLocalstat percentile output

jbarredo September 10, 2021 09:57AM

Re: 3dLocalstat percentile output

Daniel Glen September 10, 2021 12:15PM

Re: 3dLocalstat percentile output

jbarredo September 15, 2021 08:30AM