1d_tool.py: no "-csim_show_clustsize" option (ERROR): Ubuntu 14.04, AFNI Precompiled binary Debian-x86_64-1-gnu: Jan 23 2018

I am trying to get volume threshold values from ClustSim results from a NN1_bisided.1D file. My current method is trying to use 1d_tool.py and I am using the method seen in the following guide.

The line with the first error is:
set clust_thrvol = 1d_tool.py -verb 0 -infile $sid.$currtask.ClustSim.${csim_NN}_${csim_sided}.1D -csim_pthr $csim_pthr -csim_alpha "$csim_alpha"
Where clust_thrvol should equal a number (clust size) but instead gives:
** error: unknown trailing arguments : [‘-csim_pthr’, ‘0.001’, ‘-csim_alpha’, ‘0.05’]

I am running:
Ubuntu version 14.04, AFNI Precompiled binary Debian-x86_64-1-gnu: Jan 23 2018 (Version Debian-18.0.05+git24-gb25b21054~dfsg.1-1~nd14.04+1)
I was told this was the latest certified AFNI version for Ubuntu 14 (but that perhaps the latest non-packaged release could be installed). Would that help? What can I do? Is there another way I can be selecting the cluster threshold volume?



That version is old enough that I am not sure that it would have the option in question. The most recent build version of AFNI, with accompanying binaries, is from less than a week ago.

How are you getting your AFNI binaries? Is it through Neurodebian, for example? If that is the case, that version has often been several months behind the most recent one distributed by AFNI.

We describe installing AFNI on various systems here:
(but they you would want to be careful not to have conflict between different versions of packages on your computer).


That’s right. The -csim_show_clustsize option is from April 18, 2018.

  • rick

Are the options for -csim_alpha and -csim_pthr also from April 18th 2018? I am not sure how my department is getting their AFNI binaries; I am looking into that now. They mentioned they could get a newer non-packaged version, which I would assume/hope would be after April.

Thank you very much for your help!

Yes, those csim options correspond to the main clustsim one.

Your department is probably getting the newer binaries from
our site, while you are getting them from the NeuroDebian
repository. Which to use is up to you.

  • rick