Can someone clarify whether the -clustsim option within 3dttest++ is actually available for public use in afni & how specifically to implement it? I was under the impression it was, but when I attempt to use it, an error occurs saying that 3dttest++ does not recognize that option.
I’ve noticed the same thing. It’s described in the 3dttest++ help file for the version of AFNI I’m running (afni/16.1.27), but it doesn’t recognize the -clustsim flag when I try to run it.
So for me it appeared in part to be an AFNI version issue. I checked and realized we were running a few versions behind the current build. So now the -clustsim flag is recognized by AFNI when I run it. However, I am running into a different error now.
The output .BRIKs containing the results of the group analysis as well as the residual file are created successfully, but the program fails when starting the clustsim portion, giving the following error:
FATAL ERROR: Option -setA (long form): need at least 2 datasets.
So, it would appear that upon reaching the clustsim portion of the analysis, it no longer recognizes the manner in which the ttest is set up. I am confused by this because if there was a problem with the way things were set up––btw, this is supposed to be an independent samples t-test, with 2 groups (unequal size) and covariates)––then wouldn’t the output of the group analysis not be created either?
It was a similar issue for me. In my case, the script I was running that had the 3dttest++ command in it was calling an older (pre -clustsim) version of the program (for reasons I don’t understand) when I ran it with “tcsh my_script.tcsh”, but it ran the new version when I executed the script with “source my_script.tcsh”. Changes were made to our servers recently that I believe are causing this issue to arise for me.
I’ll suggest posting your entire 3dttest++ command for debugging the other error.
Here is a shortened version of the command I was running which has been giving me problems in employing the -Clustsim option in 3dttest++. I have many more subjects than I have listed here (45 in set A, 37 in set B), but have truncated the listing here for purposes of display/efficiency. Any thoughts would be more than welcome; let me know if something is unclear here.
I’m not an officially sanctioned message board troubleshooter, but the first thing I would check with the error you’re getting is that there are no spaces after the \ characters that continue the command onto the next line.
Thanks for the suggestions. I am pasting below the output from 3dttest++ beginning after the output .BRIK has already been written to the disk; I also tried the file_test command as per your last message on the script file and no problems were reported.
Fatal Signal 11 (SIGSEGV) received
THD_open_tcat
THD_open_dataset
get_options
3dClustSim
Bottom of Debug Stack
** AFNI version = AFNI_16.1.28 Compile date = Jun 30 2016
** [[Precompiled binary linux_xorg7_64: Jun 30 2016]]
** 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.
** Crash log is appended to file /space/raid/home/dfareri/.afni.crashlog
** FATAL ERROR: ===== 3dClustSim command failed :-((( =====
** Program compile date = Jun 30 2016
Can you please update your AFNI binaries and try this command again? Even if it crashes, the newer version of 3dttest++ should output more information about what it’s doing as it progresses through the -Clustsim option, and that may help debug.
Also, if any of your input filenames or labels have spaces in them (that you used quotes to input to 3dttest++), then the -Clustsim option will probably fail.
Thanks for the suggestions. I had the AFNI binaries updated and attempted to re-run the analysis. If I understand your last point regarding spaces correctly, I don’t believe that is the case, but perhaps when you see the information below you might be able to let me know.
When attempting this in the updated version of AFNI, the main group results dataset is successfully written again, as is the residuals dataset. AFter that, it appears that the 3dclustsim is starting up just fine, but then an error message appears saying that AFNI cannot open the first subbrik of the residual dataset. I find this odd because the dataset is created and I am able to view it in AFNI. I have pasted below the output from the terminal beginning with the successful writing of the group data and the start of the clustsim section immediately following (sorry for the excessive length of what is below).
Found 3 numeric columns: Age Gender Motion
** FATAL ERROR: Option -setA: can’t open dataset ‘3dttest_residuals_test_7_13_2016[0]’
** Program compile date = Jul 9 2016
Fatal Signal 11 (SIGSEGV) received
THD_open_tcat
THD_open_dataset
get_options
3dClustSim
Bottom of Debug Stack
** AFNI version = AFNI_16.2.01 Compile date = Jul 9 2016
** [[Precompiled binary linux_openmp_64: Jul 9 2016]]
** 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.
** Crash log is appended to file /space/raid/home/dfareri/.afni.crashlog
** FATAL ERROR: ===== 3dClustSim command failed :-((( =====
** Program compile date = Jul 9 2016
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