Hello,

I am trying to run a simple level 1 analysis for a task where participants were excluded or included for a block of time. The block time varied based on the individuals response times (throwing a ball to other participants). I am new to AFNI but am just trying to run a simple 3dDeconvolve analysis for one participants on fMRIprep preprocessed data. Maybe I am missing the point of this process, but not sure how to model my data when I have blocks of differing durations?

I keep getting the following error message and I can’t seem to resolve this…

*+ WARNING: ‘-stim_times_AM1 1’ didn’t read any good times from file ‘/mnt/analysis/sub-06/beh/test.1D’

++ ‘-stim_times_AM1 1 /mnt/analysis/sub-06/beh/test.1D’ has 1 auxiliary values per time point

++ ‘-stim_times_AM1 1’: basis function model ‘dmBLOCK(1)’ uses 1 parameters,

out of the 1 found in timing file ‘/mnt/analysis/sub-06/beh/test.1D’

*+ WARNING: ‘-stim_times_AM1 2’ didn’t read any good times from file ‘/mnt/analysis/sub-06/beh/tf_asd_06_equal_play.txt’

++ ‘-stim_times_AM1 2 /mnt/analysis/sub-06/beh/tf_asd_06_equal_play.txt’ has 1 auxiliary values per time point

++ ‘-stim_times_AM1 2’: basis function model ‘dmBLOCK(1)’ uses 1 parameters,

out of the 1 found in timing file ‘/mnt/analysis/sub-06/beh/tf_asd_06_equal_play.txt’

** ERROR: 3dDeconvolve dies: Unrecognized command line option: ‘SYM: +full -equal’

Here’s hoping these excerpts from ‘3dDeconvolve -help’ enlighten:

‘of the full model (all regressors) vs. the baseline model. Thus, it’

‘against the full model with just that set of regressors removed. If’

‘from the full model fit to the input data’

- what I have tried…

- changing to “dmBLOCK(0)”, “dmBLOCK(2)”, “dmBLOCK”
- changing the timing file to FSL formate and running “-stim_times_FSL”
- creating a timing file with timing_tool.py -fsl_timing_files fsl_format.txt -write_timing output.1D and then insert (you will see two different input timing files below, 1 in 1D format and the other in .txt format
- making the times smaller and the durations of increasing order in the timing file

still getting the same error???

Here is my code (I am running AFNI through docker)

subject=06

for subject in $subject; do

docker run -it -v /mnt/c/analysis/analysis/derivatives:/mnt/analysis/ afni/afni_make_build 3dDeconvolve -input /mnt/analysis/sub-${subject}/func/sub-${subject}*scale.nii.gz \
-censor censor.1D
-mask /mnt/analysis/sub-${subject}/func/sub-01_task-cyber_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz
-polort 2
-num_stimts 2
-stim_times_AM1 1 /mnt/analysis/sub-${subject}/beh/test.1D ‘dmBLOCK(1)’
-stim_label 1 full
-stim_times_AM1 2 /mnt/analysis/sub-${subject}/beh/tf_asd*${subject}_equal_play.txt ‘dmBLOCK(1)’

-stim_label 2 equal

-ortvec /mnt/analysis/sub-${subject}/func/confound_test.1D

-gltsym ‘SYM: +full -equal’

-glt_label 1 full_exclude-equal_play

-gltsym ‘SYM: +equal -full’

-glt_label 2 equal_play-full_exclude

-fout -tout -x1D X.xmat.1D -xjpeg X.jpg

-x1D_uncensored X.nocensor.xmat.1D

-fitts fitts.$subject

-errts errts.${subject}

-bucket stats.$subject

done

This runs the following in afni container…

3dDeconvolve -input /mnt/analysis/sub-06/func/sub-06_scale.nii.gz -censor censor.1D -mask /mnt/analysis/sub-06/func/sub-01_task-cyber_space-MNI152NLin2009cAsym_desc-brain_mask.nii.gz -polort 2 -num_stimts 2 -stim_times_AM1 1 /mnt/analysis/sub-06/beh/test.1D dmBLOCK(1) -stim_label 1 full -stim_times_AM1 2 /mnt/analysis/sub-06/beh/tf_asd_06_equal_play.txt dmBLOCK(1) -stim_label 2 equal -ortvec /mnt/analysis/sub-06/func/confound_test.1D -gltsym SYM: +full -equal -glt_label 1 full_exclude-equal_play -gltsym SYM: +equal -full -glt_label 2 equal_play-full_exclude -fout -tout -x1D X.xmat.1D -xjpeg X.jpg -x1D_uncensored X.nocensor.xmat.1D -fitts fitts.06 -errts errts.06 -bucket stats.06

Here is my original timing file

10:22.594 76:22.926 260:20.6