Hello,
I am trying to analyze data from a task consisting of two conditions where reaction times varied greatly: ranging from 1-30 seconds. To alleviate this, I've put trials into bins (2-sec) for each condition, and am trying to incorporate this into my design matrix. By binning my trials, I run into situations where some bins contain little data, so an example timing file may be as sparse as this:
-1*37
-1*37
-1*37
-1*37
1.02:28.95
-1*37
Currently, this is how I've set up my 3dDeconvolve command:
3dDeconvolve \
-input sub-${s}_allruns_scaled.nii.gz \
-polort A \
-jobs 1 \
-local_times \
-concat 1D: 0 870 1740 2610 3480 4350 5220 \
-allzero_OK \
-GOFORIT 9 \
-num_stimts 26 \
-stim_times_AM1 1 Timing_Files/cond-mut_bin2-4.txt 'dmBLOCK(1)' -stim_label 1 mut_2-4 \
-stim_times_AM1 2 Timing_Files/cond-mut_bin4-6.txt 'dmBLOCK(1)' -stim_label 2 mut_4-6 \
-stim_times_AM1 3 Timing_Files/cond-mut_bin6-8.txt 'dmBLOCK(1)' -stim_label 3 mut_6-8 \
-stim_times_AM1 4 Timing_Files/cond-mut_bin8-10.txt 'dmBLOCK(1)' -stim_label 4 mut_8-10 \
-stim_times_AM1 5 Timing_Files/cond-mut_bin10-12.txt 'dmBLOCK(1)' -stim_label 5 mut_10-12 \
-stim_times_AM1 6 Timing_Files/cond-mut_bin12-14.txt 'dmBLOCK(1)' -stim_label 6 mut_12-14 \
-stim_times_AM1 7 Timing_Files/cond-mut_bin14-16.txt 'dmBLOCK(1)' -stim_label 7 mut_14-16 \
-stim_times_AM1 8 Timing_Files/cond-mut_bin16-18.txt 'dmBLOCK(1)' -stim_label 8 mut_16-18 \
-stim_times_AM1 9 Timing_Files/cond-mut_bin18-20.txt 'dmBLOCK(1)' -stim_label 9 mut_18-20 \
-stim_times_AM1 10 Timing_Files/cond-mut_bin20-22.txt 'dmBLOCK(1)' -stim_label 10 mut_20-22 \
-stim_times_AM1 11 Timing_Files/cond-mut_bin22-24.txt 'dmBLOCK(1)' -stim_label 11 mut_22-24 \
-stim_times_AM1 12 Timing_Files/cond-mut_bin24-26.txt 'dmBLOCK(1)' -stim_label 12 mut_24-26 \
-stim_times_AM1 13 Timing_Files/cond-mut_bin26-28.txt 'dmBLOCK(1)' -stim_label 13 mut_26-28 \
-stim_times_AM1 14 Timing_Files/cond-mut_bin28-30.txt 'dmBLOCK(1)' -stim_label 14 mut_28-30 \
-stim_times_AM1 15 Timing_Files/cond-neu_bin2-4.txt 'dmBLOCK(1)' -stim_label 15 neu_2-4 \
-stim_times_AM1 16 Timing_Files/cond-neu_bin4-6.txt 'dmBLOCK(1)' -stim_label 16 neu_4-6 \
-stim_times_AM1 17 Timing_Files/cond-neu_bin6-8.txt 'dmBLOCK(1)' -stim_label 17 neu_6-8 \
-stim_times_AM1 18 Timing_Files/cond-neu_bin8-10.txt 'dmBLOCK(1)' -stim_label 18 neu_8-10 \
-stim_times_AM1 19 Timing_Files/cond-neu_bin10-12.txt 'dmBLOCK(1)' -stim_label 19 neu_10-12 \
-stim_times_AM1 20 Timing_Files/cond-neu_bin12-14.txt 'dmBLOCK(1)' -stim_label 20 neu_12-14 \
-stim_times_AM1 21 Timing_Files/cond-neu_bin14-16.txt 'dmBLOCK(1)' -stim_label 21 neu_14-16 \
-stim_times_AM1 22 Timing_Files/cond-neu_bin16-18.txt 'dmBLOCK(1)' -stim_label 22 neu_16-18 \
-stim_times_AM1 23 Timing_Files/cond-neu_bin18-20.txt 'dmBLOCK(1)' -stim_label 23 neu_18-20 \
-stim_times_AM1 24 Timing_Files/cond-neu_bin20-22.txt 'dmBLOCK(1)' -stim_label 24 neu_20-22 \
-stim_times_AM1 25 Timing_Files/cond-neu_bin22-24.txt 'dmBLOCK(1)' -stim_label 25 neu_22-24 \
-stim_times_AM1 26 Timing_Files/cond-neu_bin24-26.txt 'dmBLOCK(1)' -stim_label 26 neu_24-26 \
-num_glt 1 \
-gltsym 'SYM: mut_2-4 +mut_4-6 +mut_6-8 +mut_8-10 +mut_10-12 +mut_12-14 +mut_14-16 +mut_16-18 +mut_18-20 +mut_20-22 +mut_22-24 +mut_24-26 +mut_26-28 +mut_28-30 -neu_2-4 -neu_4-6 -neu_6-8 -neu_8-10 -neu_10-12 -neu_12-14 -neu_14-16 -neu_16-18 -neu_18-20 -neu_20-22 -neu_22-24 -neu_24-26' -glt_label 1 M-N \
-fout -tout -xsave \
-fout -tout -xsave \
-x1D sub-${s}.xmat.1D \
-x1D_uncensored sub-${s}.uncensor.xmat.1D \
-errts sub-${s}_errts.nii.gz \
-cbucket sub-${s}_Decon_betas.nii.gz \
-bucket sub-${s}_Decon.nii.gz
Since certain bins contain little data, I've included the --allzero_OK and -GOFORIT options, which ignores the WARNING !! issues. Although this command runs without hitting any fatal errors, I wanted to see if this is an appropriate design setup, given my data? The AFNI documentation recommends being very careful using the -GOFORIT option, so I wanted to clarify whether this seems appropriate.
Thank you for the help.
Edited 2 time(s). Last edit at 02/04/2019 03:23PM by Dan.
