AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

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kxd344
August 20, 2018 11:27AM
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?

Thanks!
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Subject Author Posted

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

kxd344 August 20, 2018 11:27AM

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

ptaylor August 20, 2018 11:54AM

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

rick reynolds August 20, 2018 12:00PM

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

kxd344 August 21, 2018 11:20AM

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

rick reynolds August 21, 2018 12:06PM