Changed username on Ubuntu bionic - afni command not found

AFNI Message Board
1

Hello all,

I am very, very new to the AFNI community and to using the Linux terminal.

I had AFNI installed on my Ubuntu 18.04 and it was working great, but I changed the username on the machine. Now everything else is fine, including FSL, but when I try to access AFNI it suddenly says command not found.

I tired following the instructions on installing it again to trace the error, I got to this stage “tcsh @update.afni.binaries -package linux_ubuntu_16_64 -do_extras” and when it got to installing the new binaries, it gave the following error “home/phoenix*/.bash_profile: No match”. There is probably a very simple solution to this, but I am really new to Linux and I would appreciate any help here.

Thank you all!
Best,
Petya

2

Hi, Petya-

A few questions:

A) When you set up AFNI, did you follow the default instructions from here:
https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_ubuntu18.html
?
(My guess is that when you install FSL, it is in “/usr/bin” or somewhere like that, while the AFNI “abin” of binaries goes into your home directory, so your $PATH variable, which tells your shell where to find programs, might have the outdated name or something.)

And what are the outputs of the following (you can copy/paste each into a terminal):

B)


cd ; ls

C)


echo $0

D)


echo $PATH

E)


grep -H abin ~/.*rc

thanks,
pt

3

Hello,

Thank you for the help here.
A - yes, I followed the instructions on the website.

B


abin                          Pictures
@add_rcran_ubuntu_18.04.tcsh  Public
CD                            R
CD.tgz                        rstudio-server-1.2.5042-amd64.deb
dcm2niix_lnx.zip              std_meshes
Desktop                       suma_demo
Documents                     Templates
Downloads                     @update.afni.binaries
examples.desktop              @update_rcran.R
Firefox_wallpaper.png         Videos
Music

C
bash

D


/usr/local/fsl/bin:/home/phoenix*/.local/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin:/home/petyakozhuharova/abin

E


/home/phoenix*/.afnirc:// AFNI_PLUGINPATH          = /home/rwcox/abin  // dir for plugins
/home/phoenix*/.afnirc:// AFNI_MODELPATH           = /home/rwcox/abin  // dir for NLfim models
/home/phoenix*/.bashrc:export PATH=$PATH:/home/petyakozhuharova/abin
/home/phoenix*/.cshrc:set path = ( $path  /home/petyakozhuharova/abin  ) 
/home/phoenix*/.cshrc:set path = ( $path ~/abin )
/home/phoenix*/.cshrc:set path = ( $path ~/abin )

Best,
Petya

4

Hello,

Thank you so much for the reply! Once you gave me an indication of where the issue is and how to check the paths I got it sorted. I changed the paths specified in the bashrc files and AFNI works fine again, both command line and GUI! Thank you so very much!

Hopefully this is the issue sorted for good now!
Best wishes,
Petya

5

Hi, Petya-

OK, yes, I think it was just a matter of dealing with these files/variables:


/home/phoenix*/.bashrc:export PATH=$PATH:/home/petyakozhuharova/abin
/home/phoenix*/.cshrc:set path = ( $path  /home/petyakozhuharova/abin  )

… changing the location of abin to have your new username-- glad you have sorted it, then!

Note that you can also run the system check again:


afni_system_check.py -check_all

… just to be sure everything with the setup is happy.

–pt