Hello,

I am noticing some warning message that I don't fully understand, and am worried are affecting the output. I run 3dDeconvolve after using 3dTcat to combine the functional runs (following intensity normalization) into one file. The 3dDeconvolve command I'm using is:
3dDeconvolve \
-input $data_dir/$s/fmriprep/sub-${s}/func/*smooth_scale_all* \
-polort A \
-jobs 1 \
-ortvec $data_dir/$s/fmriprep/sub-${s}/func/sub-${s}*confounds_noheader_all.1D \
-local_times \
-concat '1D: 0 870 1740 2610 3480 4350 5220 5513' \
-num_stimts 2 \
-stim_times_AM2 1 $data_dir/$s/derivatives/Timing_Files/AM/mut.txt 'dmBLOCK(1)' -stim_label 1 mut \
-stim_times_AM2 2 $data_dir/$s/derivatives/Timing_Files/AM/neu.txt 'dmBLOCK(1)' -stim_label 2 neu \
-num_glt 1 \
-gltsym 'SYM: mut -neu' -glt_label 1 M-N \
-fout -tout \
-x1D $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}.xmat.1D \
-x1D_uncensored $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}.uncensor.xmat.1D \
-errts $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}_errts \
-fitts $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}_fitts \
-cbucket $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}_Decon_betas.nii.gz \
-bucket $data_dir/$s/fmriprep/sub-${s}/func/zsub-${s}_Decon.nii.gz


This is some of the output I'm getting on the command line:

++ '-stim_times_AM2 1 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/mut.txt' has 1 auxiliary values per time point
++ '-stim_times_AM2 1': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 1 found in timing file '/N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/mut.txt'
*+ WARNING: '-stim_times_AM2 1 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/mut.txt' has 0 amplitude modulation parameters; ==> converting to be like -stim_times_AM1
++ '-stim_times_AM2 1 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/mut.txt' will have 1 regressors
++ '-stim_times_AM2 2 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/neu.txt' has 1 auxiliary values per time point
++ '-stim_times_AM2 2': basis function model 'dmBLOCK(1)' uses 1 parameters,
out of the 1 found in timing file '/N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/neu.txt'
*+ WARNING: '-stim_times_AM2 2 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/neu.txt' has 0 amplitude modulation parameters; ==> converting to be like -stim_times_AM1
++ '-stim_times_AM2 2 /N/dc2/scratch/dlevitas/fMRI_data/std/002/derivatives/Timing_Files/AM/neu.txt' will have 1 regressors
++ 3dDeconvolve extending num_stimts from 2 to 31 due to -ortvec
++ 3dDeconvolve: AFNI version=AFNI_18.0.12 (Feb 5 2018) [64-bit]
++ Authored by: B. Douglas Ward, et al.
++ current memory malloc-ated = 3,528,121 bytes (about 3.5 million [mega])
++ loading dataset /N/dc2/scratch/dlevitas/fMRI_data/std/002/fmriprep/sub-002/func/sub-002_task-std_bold_space-MNI152NLin2009cAsym_preproc_smooth_scale_all.nii.gz
++ current memory malloc-ated = 3,528,121 bytes (about 3.5 million [mega])
++ STAT automask has 325321 voxels (out of 325325 = 100.0%)
++ Skipping check for initial transients
++ Imaging duration=365.4 s; Automatic polort=3
++ -stim_times using TR=0.42 s for stimulus timing conversion
++ -stim_times using TR=0.42 s for any -iresp output datasets
++ [you can alter the -iresp TR via the -TR_times option]
++ ** -stim_times NOTE ** guessing GLOBAL times if 1 time per line; LOCAL otherwise
++ ** GUESSED ** -stim_times_AM2 1 using LOCAL times
*+ WARNING: '-stim_times_AM2 1' (LOCAL) run#7 has 5 times outside range 0 .. 122.64 [PSFB syndrome]
+ dataset TR being used is 0.42 s -- unusable times follow
135.32 194.16 211.6 255.4 289.36
++ ** GUESSED ** -stim_times_AM2 2 using LOCAL times
*+ WARNING: '-stim_times_AM2 2' (LOCAL) run#7 has 4 times outside range 0 .. 122.64 [PSFB syndrome]
+ dataset TR being used is 0.42 s -- unusable times follow
124.36 172.48 231.33 318.64
------------------------------------------------------------
GLT matrix from 'SYM: mut -neu':
0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 -1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0

++ Number of time points: 6383 (no censoring)
+ Number of parameters: 63 [61 baseline ; 2 signal]

The first set of warnings are in relation to stim_times_AM2. I am interested in both duration and amplitude modulation (hence why I'm using stim_times_AM2); however, the warning message says that the program will use stim_times_AM1 instead. Is there a way to prevent this?

The second set of warning pertains to the timing in my run #7 that are apparently outside range 0...122.64. This is confusing to me because my run #7 contains the full number of volumes (870) as the previous ones, so unless there is an issue with my timing files, I was wondering if there is something else I need to do?

Thank you for the assistance.

Dan