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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April 28, 2022 04:24PM
Howdy ptaylor,
Thanks for the tips. I was able to create the mask with just one voxel, I believe, and a picture of this can be seen in the attachment to this file. However, when I go to use the 3dmaskave command, like so:

bash-3.2$ 3dmaskave -quiet -mask tmp_mask+tlrc /Users/reynaadmin/test.results/Ado_Updated_LargeRewardSmallReward_GroupHungerRegress+tlrc.BRIK[1]
++ 3dmaskave: AFNI version=AFNI_22.0.10 (Feb 15 2022) [64-bit]
+++ 1 voxels survive the mask
0

The command outputs a value of 0. I've tried several variations of the code and I just kept on getting 0, so I figured it was time to turn to the afni gods once more.

Also attached to this document is the 3dinfo -verb output for the .Brik file I am testing on. The Thr= value for the first peak cluster coordinate is around -3.579. Below is the code that I ran based on your suggestions:

1dcat o.peak_coords.txt'{0}' | 3dUndump -master /Users/reynaadmin/test.results/Ado_Updated_LargeRewardSmallReward_GroupHungerRegress+tlrc.BRIK -xyz -overwrite -prefix tmp_mask -

3dmaskave -quiet -mask tmp_mask+tlrc /Users/reynaadmin/test.results/Ado_Updated_LargeRewardSmallReward_GroupHungerRegress+tlrc.BRIK[1]

Thanks again for all the help,
-Rookie
Attachments:
open | download - Screen Shot 2022-04-28 at 4.18.34 PM.png (1.68 MB)
open | download - Screen Shot 2022-04-28 at 4.15.44 PM.png (784.3 KB)
Subject Author Posted

How to automate getting Peak t Cluster Values Attachments

Rookie April 27, 2022 01:52PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 27, 2022 03:26PM

Re: How to automate getting Peak t Cluster Values Attachments

Rookie April 27, 2022 04:02PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 27, 2022 05:55PM

Re: How to automate getting Peak t Cluster Values Attachments

Rookie April 28, 2022 04:24PM

Re: How to automate getting Peak t Cluster Values

Rookie April 30, 2022 12:55PM

Re: How to automate getting Peak t Cluster Values

ptaylor April 30, 2022 07:48PM