Hi, I am trying to utilize 3dGroupCorr. I am not sure of my commands are correct since the option to perform the operation is not coming up (see commands below).

Any guidance would be greatly appreciated. Thanks!

shiva:/x/wmg15/jasmins/STRUCTSpt/GrpResults> afni -niml template_T1_dartel_strip_240sagvols_1.5mm_MNI.nii
Precompiled binary linux_openmp_64: Aug 19 2020 (Version AFNI_20.2.13 ‘Aulus Vitellius’)

** Version check disabled: AFNI_VERSION_CHECK forbids
Thanks go to P Taylor for caloric input

Initializing: X11[Moba/X v 12004000]… Widgets… Input files:
session # 1 = fromCLI ==> 1 dataset
dataset count = 1
Time series = 0 files read
.[tc]sv data = 0 files read
Path(s) to be searched for plugins:

Plugins = 50 libraries read

++ NOTICE: AFNI_ENFORCE_ASPECT no longer has any effect!

++ Can’t find program ffmpeg for Save to MPEG-1
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to ‘NO’.

++ NOTE: This version of AFNI was built Aug 19 2020 ++
++ NOTE: ‘Define Markers’ is hidden: right-click ‘DataDir’ to see it
++ NOTE: Use ‘-seehidden’ option to see which plugins are hidden
++ Want your picture in the AFNI splash screen? Email us a square JPEG!

------------------------- AFNI Startup Tip (74/109)----------------------------
Want bigger fonts in AFNI, for a high resolution screen? Set environment
variable AFNI_FONTSIZE to PLUS or BIG (preferably in your .afnirc setup file).

tcp_listen(bind) (Name AFNI_SUMA_NIML, Port 53211, sd 5): Address already in use
tcp_listen(bind) (Name AFNI_DEFAULT_LISTEN_NIML, Port 53212, sd 5): Address already in use
tcp_listen(bind) (Name AFNI_GroupInCorr_NIML, Port 53213, sd 5): Address already in use
++ NIML shutting down: no listening sockets
3dGroupInCorr -setA globalETAC.mthresh.ttest_FALFF.HVs_F74s.default.ETAC.A.5perc.niml


You are getting an “Address already in use” error. That means there is some other “afni -niml” process running on that computer (possibly by you, but it could be someone else).

First ask for an available NIML port block, and then apply it with -npb. So consider these commands:

afni -available_npb

(and supposing this says "2" is the first available npb)

afni -npb 2 -niml
3dGroupInCorr -npb 2 ....

Does that seem reasonable?

  • rick

Hi Rick, thank you!

The first two commands work.
afni -available_npb
afni -npb 1 T1_dartel_avg_240sagvols_1.5mm_MNI.nii

However, the third one does not. This is the error message.

      3dGroupInCorr -npb 1 -setA globalETAC.mthresh.ttest_FALFF.HVs_F74s.default.ETAC.A.5perc.niml

This is the error message:

Fatal Signal 6 (SIGABRT) received
Bottom of Debug Stack
** Command line was:
3dGroupInCorr -setA globalETAC.mthresh.ttest_FALFF.HVs_F74s.default.ETAC.A.5perc.niml
** AFNI version = AFNI_21.0.06 Compile date = Jan 26 2021
** [[Precompiled binary linux_centos_7_64: Jan 26 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.
** Crash log is appended to file /home/jasmins/.afni.crashlog
[jasmins@cn0929 GrpResults_HVs]$