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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November 15, 2022 12:03PM
Dear afni experts,

I'd like to use 3dDeconvolve with a block-design paradigm. Each functional run consists of an active block (3 minutes), short break (20 seconds) and a passive block (3 minutes) lasting for 380 seconds in total. The TR is 2.5 s and there are 3 functional scans each of which with 152 volumes. I have used the following arguments to run the command which works with no errors. However, when I plot run-all_X.xmat.1D, the predicted fit for the active block does not match the stimulus timing in 'stim_active.txt' (see the attachments). Based on the plot, it seems that the active block was on during the whole run i.e. form volume 0 to 151 while the .txt file shows that it ends at 180 seconds. I'm not sure what has gone wrong here and would greatly appreciate hearing your thoughts. Thank you!

3dDeconvolve -input run-all.nii.gz \
-concat '1D: 0 152 304' \
-polort 3 \
-num_stimts 2 \
-stim_times 1 stim-active.txt 'BLOCK(180,1)' -stim_label 1 Active \
-stim_times 2 stim-passive.txt 'BLOCK(180,1)' -stim_label 2 Passive \
-gltsym 'SYM: Active -Passive' -glt_label 1 A-P \
-tout -x1D run-all_X.xmat.1D -xjpeg run-all_X.jpg \
-fitts run-all_fitts -bucket run-all_func \
-jobs 10
Attachments:
open | download - 1.png (4.4 KB)
open | download - stim-active.png (142 KB)
Subject Author Posted

Design matrix and 3dDeconvolve Attachments

Khazar November 15, 2022 12:03PM

Re: Design matrix and 3dDeconvolve

rick reynolds November 15, 2022 01:43PM