-Clustsim on 3dttest++

AFNI Message Board
1

Hello,

I am new to AFNI and am trying to run 3DClustSim, but read how I can run a paired t-test used 3dttest++ invoking -Clustsim

I tried the following: [b]3dttest++ -Clustsim -AminusB -prefix /{path to group difference file}
-setA \
{files}
-setB [/b]

but that doesn’t seem to work, any suggestions on how to include -Clustsim in my script?

Thank you so much!!

2

In what way doesn’t it work? Do you get any Warning or Error messages? In situations like this, it helps a lot if you can copy/paste the screen output text from the program to help diagnose what exactly happened.

3

For example, when I try a command similar to yours, I get:


++ 3dttest++: AFNI version=AFNI_22.0.21 (Mar 21 2022) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
++ option -setA :: processing as SHORT form (all values are datasets)
++ have 28 volumes corresponding to option '-setA'
++ option -setB :: processing as SHORT form (all values are datasets)
++ have 28 volumes corresponding to option '-setB'
** FATAL ERROR: Cannot use -Clustsim when -prefix has an absolute path
** Program compile date = Mar 21 2022

This clearly tells me what the problem is – the ‘-prefix’ option starts with a ‘/’ character.

4

Sorry about that, thank you for trying the command for me.

When I try with ‘/prefix’ I get the following:
++ 3dttest++: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
** FATAL ERROR: 3dttest++: don’t recognize option ‘/prefix’ (argv[3])
** Program compile date = Dec 30 2021
Permission denied.
-setB: Command not found.

When I try with ‘-prefix’, I get:
++ 3dttest++: AFNI version=AFNI_21.3.17 (Dec 30 2021) [64-bit]
++ Authored by: Zhark++
++ Number of -Clustsim threads set to 8
Fatal Signal 11 (SIGSEGV) received
EDIT_empty_copy
THD_open_tcat
THD_open_dataset
3dttest++ main
Bottom of Debug Stack
** AFNI version = AFNI_21.3.17 Compile date = Dec 30 2021
** [[Precompiled binary macos_10.12_local: Dec 30 2021]]
** Program Death **
** If you report this crash to the AFNI message board,
** please copy the error messages EXACTLY, and give
** the command line you used to run the program, and
** any other information needed to repeat the problem.
** You may later be asked to upload data to help debug.

5

What is your exact command that failed? Could you please copy+paste it?

–pt