Hi experts,
I am running 3dDeconvolve on data from a task with 6 conditions. Data was collected with a block design that consisted of 5 runs, with 1 block of each condition per run. Each run is 160s long, so total scanning time is 800s. When taking a look at the design matrix files (X.xmat.1D, X.nocensor.xmat.1D, X.jpg) generated by 3dDeconvolve, I noticed that blocks from run 1 are not being modeled (see attached files, first block should occur at 4s). The time axis in X.nocensor.xmat.1D matches what I would expect (800s), but there are only 4 events modeled for each condition when there should be 5. The timing of the events matches what I would expect for blocks in runs 2-5. This is happening for all subjects. Please let me know if you have any suggestions. Below is my 3ddeconvolve code and an example stim_times file

3dDeconvolve -input $parDir/func/*foodcue*${temp}*blur6-scale.nii \
-censor $parDir/func/${subID}_foodcue-allruns_censor_${TRcen}.tsv \
-mask $parDir/func/foodcue_full_mask*${temp}*.nii \
-polort 2 \
-num_stimts 21 \
-stim_times 1 $onsetDir/${subID}_HighLarge*.txt 'BLOCK(18,1)' \
-stim_label 1 HighLarge \
-stim_times 2 $onsetDir/${subID}_HighSmall*.txt 'BLOCK(18,1)' \
-stim_label 2 HighSmall \
-stim_times 3 $onsetDir/${subID}_LowLarge*.txt 'BLOCK(18,1)' \
-stim_label 3 LowLarge \
-stim_times 4 $onsetDir/${subID}_LowSmall*.txt 'BLOCK(18,1)' \
-stim_label 4 LowSmall \
-stim_times 5 $onsetDir/${subID}_OfficeLarge*.txt 'BLOCK(18,1)' \
-stim_label 5 OfficeLarge \
-stim_times 6 $onsetDir/${subID}_OfficeSmall*.txt 'BLOCK(18,1)' \
-stim_label 6 OfficeSmall \
-stim_file 7 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[0]' -stim_base 7 -stim_label 7 trans_x_01 \
-stim_file 8 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[1]' -stim_base 8 -stim_label 8 trans_y_01 \
-stim_file 9 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[2]' -stim_base 9 -stim_label 9 trans_z_01 \
-stim_file 10 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[3]' -stim_base 10 -stim_label 10 rot_x_01 \
-stim_file 11 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[4]' -stim_base 11 -stim_label 11 rot_y_01 \
-stim_file 12 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[5]' -stim_base 12 -stim_label 12 rot_z_01 \
-stim_file 13 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[6]' -stim_base 13 -stim_label 13 csf \
-stim_file 14 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[7]' -stim_base 14 -stim_label 14 white_matter \
-stim_file 15 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[8]' -stim_base 15 -stim_label 15 glob_signal \
-stim_file 16 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[9]' -stim_base 16 -stim_label 16 trans_x_02 \
-stim_file 17 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[10]' -stim_base 17 -stim_label 17 trans_y_02 \
-stim_file 18 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[11]' -stim_base 18 -stim_label 18 trans_z_02 \
-stim_file 19 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[12]' -stim_base 19 -stim_label 19 rot_x_02 \
-stim_file 20 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[13]' -stim_base 20 -stim_label 20 rot_y_02 \
-stim_file 21 $parDir/func/${subID}_foodcue-allruns_confounds-header.tsv'[14]' -stim_base 21 -stim_label 21 rot_z_02 \
-gltsym 'SYM: HighLarge -HighSmall' -glt_label 1 HighLarge-Small \
-gltsym 'SYM: LowLarge -LowSmall' -glt_label 2 LowLarge-Small \
-gltsym 'SYM: HighLarge -LowLarge' -glt_label 3 LargeHigh-Low \
-gltsym 'SYM: HighSmall -LowSmall' -glt_label 4 SmallHigh-Low \
-gltsym 'SYM: HighLarge LowLarge -HighSmall -LowSmall' -glt_label 5 Large-Small_allED \
-gltsym 'SYM: HighLarge HighSmall -LowLarge -LowSmall' -glt_label 6 High-Low_allPS \
-gltsym 'SYM: .5*HighLarge .5*HighSmall .5*LowLarge .5*LowSmall -OfficeLarge -OfficeSmall' -glt_label 7 Food-Office \
-jobs 8 \
-fout -tout -x1D X.xmat.1D -xjpeg X.jpg \
-x1D_uncensored X.nocensor.xmat.1D \
-fitts fitts.$subID \
-errts errts.$subID \
-bucket stats.$subID

Example stim_times file $onsetDir/${subID}_HighLarge*.txt (the space between the onset time and * is always a tab):
4.0 *
108.0 *
126.0 *
108.0 *
30.0 *



Edited 2 time(s). Last edit at 09/27/2022 02:48PM by bfuchs.