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  

|
November 01, 2019 06:48PM
Hello - I am still pretty new to afni. Currently, I am using the TENT function to model BOLD in a block style task. The stimulus times are stacked according to the order of runs in the first column of each text file. When writing the script and flagging -Local times I get the error below:

++ ** GUESSED ** -stim_times 1 using GLOBAL times
*+ WARNING: '-stim_times 1' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 2 using GLOBAL times
*+ WARNING: '-stim_times 2' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 3 using GLOBAL times
*+ WARNING: '-stim_times 3' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 4 using GLOBAL times
*+ WARNING: '-stim_times 4' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 5 using GLOBAL times
*+ WARNING: '-stim_times 5' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 6 using GLOBAL times
*+ WARNING: '-stim_times 6' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 7 using GLOBAL times
*+ WARNING: '-stim_times 7' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?
++ ** GUESSED ** -stim_times 8 using GLOBAL times
*+ WARNING: '-stim_times 8' (GLOBAL) has 2 runs and 2 early events; do you want LOCAL times?

Stim Files are (in ms) for Run1 and Run2 by Block onset in each run:
7.8
134.0

Here is how I scripted it:
3dDeconvolve -input files_by_run.nii \
-polort A \
-num_stimts 8 \
-CENSORTR 1:0..4 \
-CENSORTR 2:0..4 \
-ortvec ${subject}_MovReg.txt motion \
-ortvec ${subject}_CSFReg.txt csf \
-ortvec ${subject}_WMReg.txt wm \
-ortvec ${subject}_WM_GSR_Reg.txt \
-local_times \
-stim_times 1 ${subject}b1.txt 'TENT(0, 30.96,44)' -stim_label 1 b1 \
-stim_times 2 ${subject}b2.txt 'TENT(0, 30.96,44)' -stim_label 2 b2 \
-stim_times 3 ${subject}b3.txt 'TENT(0, 30.96,44)' -stim_label 3 b3 \
-stim_times 4 ${subject}b4.txt 'TENT(0, 30.96,44)' -stim_label 4 b4 \
-stim_times 5 ${subject}b5.txt 'TENT(0, 30.96,44)' -stim_label 5 b5 \
-stim_times 6 ${subject}b6.txt 'TENT(0, 30.96,44)' -stim_label 6 b6 \
-stim_times 7 ${subject}b7.txt 'TENT(0, 30.96,44)' -stim_label 7 b7 \
-stim_times 8 ${subject}b8.txt 'TENT(0, 30.96,44)' -stim_label 8 b8 \
-iresp 1 b1.nii
-iresp 2 b2.nii
-iresp 3 b3.nii
-iresp 4 b4.nii
-iresp 5 b5.nii
-iresp 6 b6.nii
-iresp 7 b7.nii
-iresp 8 b8.nii
-num_glt 12 \
-gltsym "desired contrasts here" label_for contrast \
-rout \
-tout \
-bucket FIR_model_stats.nii \
-GOFORIT 100 \
-noFDR \
-nocout \
-errts Residuals.nii \
-allzero_OK \
-jobs 10

Is there an issue I can change in the way I have organized the 3dDeconvolve commands so I can force the apropriate flag -local_times since the way I have done it (flagged -local_times before stim inputs) does not seem to work?
Subject Author Posted

3dDeconvolve -Local Times

mpipoly November 01, 2019 06:48PM

Re: 3dDeconvolve -Local Times

rick reynolds November 06, 2019 09:05AM