a silly question on AFNI installation

AFNI Message Board
1

Hi, list Experts,

I used AFNI for a while, but now I try to install it to another computer, I meet a lot of problems. Can anyone advise me?

I follow the instruction here: https://afni.nimh.nih.gov/pub/dist/doc/htmldoc/background_install/install_instructs/steps_linux_Fed_RH.html

1)Install prerequisite packages.

sudo yum install -y tcsh libXp openmotif gsl xorg-x11-fonts-misc
PyQt4 R-devel netpbm-progs gnome-tweak-tool ed
libpng12
sudo yum update -y

The problem go as following.
Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
This system is registered to Red Hat Subscription Management, but is not receiving updates. You can use subscription-manager to assign subscriptions.
Setting up Install Process
No package openmotif available.
No package gsl available.
No package R-devel available.
No package netpbm-progs available.
No package gnome-tweak-tool available.
No package libpng12 available.
Nothing to do
Loaded plugins: product-id, refresh-packagekit, security, subscription-manager
This system is registered to Red Hat Subscription Management, but is not receiving updates. You can use subscription-manager to assign subscriptions.
Setting up Update Process
No Packages marked for Update

2. Set “tcsh” to be the default shell.
chsh -s /usr/bin/tcsh

chsh: “/usr/bin/tcsh” does not exist.

3.Install AFNI.

curl -O https://afni.nimh.nih.gov/pub/dist/bin/linux_fedora_21_64/@update.afni.binaries

tcsh @update.afni.binaries -package linux_openmp_64 -do_extras

This step is fine.

4. reboot
I did this.

5.Get R setup.
tcsh
setenv R_LIBS $HOME/R
mkdir $R_LIBS
echo ‘setenv R_LIBS ~/R’ >> ~/.cshrc
rPkgsInstall -pkgs ALL

Error appears
rPkgsInstall: Command not found.

6.Automatically set up AFNI/SUMA profiles.
cp $HOME/abin/AFNI.afnirc $HOME/.afnirc
cp: cannot stat `/home/Juanw/abin/AFNI.afnirc’: No such file or directory

I do not go further. When I input “afni” in the terminal, it shows
-bash: afni: command not found.

Any good ideas for me?

2

HI, List experts,

I still can not make the AFNI run. Anyone can help me?

Following the suggestion, from my home directory, I downloaded the file: wget http://afni.nimh.nih.gov/pub/dist/bin/linux_xorg7/@update.afni.binaries

Then I used the script to execute it: tcsh @update.afni.binaries -package linux_openmp_64

Then echo command: echo ‘set path = ( $path ~/abin )’ >> .cshrc

All worked well. However, when I opened a new terminal and type afni, it always showed
-bash: afni: command not found.

I suspect that the step “tcsh @update.afni.binaries” is wrong, as when I type, “echo $0”, the output is -bash in my redhat computer. Of course, I use the ssh shell to link the Linux computer from my local Windows.

Any suggestion?

Thank you very much,
Juan

3

Hi Juan,

You have a RedHat system, and should contact them
to set up your Subscription Management service.
That is what RedHat requires to download packages
via ‘yum’ and such, as you are trying to do.

For example, you probably do not even have ‘tcsh’
on your system (try “which tcsh”).

Please contact RedHat to set that up.

  • rick
4

Hi, Rick,

Thanks for your message. I just checked two things below.

  1. which tcsh
    /bin/tcsh

So it means I have tcsh.

  1. cat /proc/version
    Linux version 2.6.32-504.16.2.el6.x86_64 (mockbuild@x86-028.build.eng.bos.redhat.com) (gcc version 4.4.7 20120313 (Red Hat 4.4.7-9) (GCC) ) #1 SMP Tue Mar 10 17:01:00 EDT 2015

My question is how to contact RedHat to set up my Subscription Management service. I do not know this. Can you give me some advice? Besides, is that possible that I directly use “yum” to download the AFNI and install it? Any good pointers?

I look forward to hearing from you. Thank you very much.
Juan

5

Hi Rick,

Do you have any suggestion for me if I want to install AFNI to NeuroDebian - I just installed an Oracle VM VirtualBox Manager to my Windows computer.

Thanks for your time,
Juan

6

Hi Juan,

Please let us know how the AFNI_Bootcamp_32.ova package works!

Thanks,

  • rick
7

Hello, Rick and list experts,

I have now installed AFNI to my linux box. The version is “AFNI_16.2.16”.

In the past years, I always use “Version AFNI_2011_12_21_1014”. The “main difference” from my quick check is that once I open the new afni, it automatically shows the three images (axial, sagittal, and coronal). Previously, it only shows the former two images. I do not know the other important difference, as I have not tried too much. However, I have now met a new problem. When I right click the image to show “where am i”, all the images suddenly disappear. What is the secret? How can I solve this problem?

When I directly go to use the Linux computer, the “where am I” works there. I use ssh secure shell from a Win 7 windows computer to link to my Linux computer. Is this the problem? However, with the version “Version AFNI_2011_12_21_1014”, my ssh secure shell works very well. Any good pointers?

Thanks so much,
Juan