3dTstat warning

AFNI Message Board
1

Hi there.
I’d like to confirm that a warning message in my output.proc file is ok to ignore.
It is in the outcount autoblock at the very beginning of pre-processing. The warning states that the input dataset is not 3d+time, and it will therefore assume the TR = 1.0. Since the input file is the 1D outcount file, I am assuming this is just a stock warning for situations in which input files are not 3d+time?

I’d just like to confirm that the script will not go on to assume that the TR =1.0 for the functional runs, correct?

Error shown below, and thank you in advance for the clarification!!


set minindex = `3dTstat -argmin -prefix - outcount_rall.1D\'
3dTstat -argmin -prefix - outcount_rall.1D'
++ 3dTstat: AFNI version=AFNI_19.2.26 (Sep 24 2019) [64-bit]
++ Authored by: KR Hammett & RW Cox
e[7m*+ WARNING:e[0m Input dataset is not 3D+time; assuming TR=1.0
set ovals = ( `1d_tool.py -set_run_lengths $tr_counts                       
                          -index_to_run_tr $minindex` )
1d_tool.py -set_run_lengths 108 108 -index_to_run_tr 127
set minoutrun = 02
set minouttr = 19
echo min outlier: run 02, TR 19
tee out.min_outlier.txt
min outlier: run 02, TR 19
foreach run ( 01 02 )
2

Hi-

Yes, that is ignorable. The “TR” field still exists for t-stat dsets (for any 4D dataset), but it won’t be used for anything.

I believe that warning is shown for all concatenation processes if a TR isn’t specified; in this case, that has no effect on anything, because ‘time’ doesn’t matter in this kind of 4D dataset.

–pt

3

Thanks for confirmation!

4

There are a few of the statistics that 3dTstat computes that depend on knowing the correct TR. But only a very few. For the vast majority, including what you have given as an example, knowing the TR is not needed. But the program puts out the WARNING just in case, since it isn’t clever enough to decide when the message is actually needed.