NITRC JIP fMRI Analysis Toolkit Forum: open-discussion

RE: JIP installation on windows

Joseph Mandeville — Tue, 19 Jul 2011 23:06:11 GMT

Hi Alessandra,

I download Cygwin/x through the main site: www.cygwin.com.
The direct link is x.cygwin.com. As I recall (it's been some time),
I used the default download. Click on the "setup.exe" link to download
a setup file, and then choose "Install from web". The documentation on the site is good.

To compile jip, you need
1) a unix/Linux environment (Cygwin), and
2) X11 libraries. The required files will be found in /usr/X11R6/lib and /usr/X11R6/include under the cygwin folder.

Hopefully the makefiles that I provide will work without modification.
If you install jip code in "jip-main", then try this:
cd jip-main/build-jip
tcsh
source build-all.tcsh

That will try to build everything, including the required NIFTI, ZLIB, and FFTW components.

Best,
Joe

JIP installation on windows

Alessandra Paladini — Fri, 08 Jul 2011 8:29:09 GMT

Hi, I need to install JIP on windows (windows 7 32 bit).
Can you provide me some installation Instruction? I see that I need Cgwin to install it, can you suggest me the best version to download?
Thank you in advance,
Alessandra

RE: Welcome to Open-Discussion

Joseph Mandeville — Wed, 23 Feb 2011 22:42:48 GMT

Hi Katelin,

On Linux, executables are invoked from the command line by referencing the name of the executable with an interpretable path. So, if jip-display is sitting on /home/katelin/jip-current/jip-display/Linux-x86_64, then you can run it by typing
/home/katelin/jip-current/jip-display/Linux-x86_64/jip-display or ~katelin/jip-current/jip-display/Linux-86_64/jip-display.

I set up executables to run through shell scripts, which provide a number of advantages:
1) aliases are defined so that you don't have to type as much,
2) If you switch from a 64-bit machine to a 32-bit machine, you don't have to change anything (the 32-bit executable will be used),
3) an environment variable is defined (JIP_HOME), which enables programs to find help files.

I strongly suggest doing this:

Let's say that you now have a directory named /home/katelin/jip-current:
1) If you are using the tcsh or csh Linux shell, then edit the file /home/katelin/jip-current/define-jip.tcsh
   If you are using the bash Linux shell, then edit the file /home/katelin/jip-current/define-jip.bash
   In either case, use the editor to change the directory name corresponding to JIP_HOME to point to the directory /home/katelin/jip-current
2) To define jip executables, do this:
   source /home/katelin/jip-current/define-jip.tcsh
   This Linux script will tell you the names of aliases that have been defined. For instance, xd points to the display package.
   If you have a NIFTI file "myfile.nii", then you can display it from Linux by typing "xd myfile.nii"
3) So that you don't have to "source" the script every time you login, put this into your .cshrc:
   source /home/katelin/jip-current/define-jip.tcsh 1
   The "1" at the end simply suppresses output, so that don't get messages from "define-jip.tcsh" every time you login.
   If you are using the bash shell, do exactly the same thing but replace "define-jip.tcsh" with "define-jip.bash"

That should do it.
If you other questions on this subject, please contact me directly (jbm@nmr.mgh.harvard.edu).

Best,
Joe

RE: Welcome to Open-Discussion

Katelin Engerer — Wed, 23 Feb 2011 21:22:35 GMT

OK, you'll have to forgive me if these are really basic questions but I'm new to the image processing world. I'd like to use your JIP program to look at some BOLD data from rats and I don't really know where to begin. I've downloaded the program and put it in my home path as it said to do in the read me file but now I'm at a standstill. Is there an executable file I can run? I'm on a 64bit Linux system running Suse if that helps, but when I click the exectuable files in the folders I downloaded nothing happens.

Thanks for any help!
Katelin

RE: bash shell definition script

Joseph Mandeville — Mon, 24 Jan 2011 1:28:39 GMT

erratum: One needs to "source" the script in the tcsh, just like in the bash shell.

% tcsh
% source define-jip.tcsh

Sorry for the confusion. This is described correctly in README.jip on the main jip directory.

bash shell definition script

Joseph Mandeville — Wed, 19 Jan 2011 16:16:09 GMT

In the distributions to date, a script "define-jip.tcsh" is included.
To use this script successfully, one must be working in the tcsh shell.
If you are not using this shell, you have two options:

1) Switch to tcsh like this ("%" represents the Unix/Linux prompt):
% tcsh
% define-jip.tcsh
... or put these definitions into your .cshrc startup file. Use any argument to suppress output:
source absolute_path/define-jip.tcsh 1

2) Modify the script for your particular Unix/Linux shell. For example, a bash script is shown
below. You must SOURCE this script, like this:
source define-jip.bash
but NOT like this:
./define-jip.bash
The latter method only creates temporary definitions in the scripting shell, not the working shell.
As with define-jip.tcsh, you can put this into your startup file (.bashrc) like this
source absolute_path/define-jip.bash 1

Here is "define-jip.bash"
-----------------------------------------------------------------------
#!/bin/bash
# Include any argument to suppress output. E.g.,
# source ~jbm/jip-current/define-jip.script 1
# from startup file .bashrc

# Set the JIP_HOME environment variable to access documentation from programs.
# e.g., xd -H
export JIP_HOME=/Users/jbm/Unix/jip-new
# These aliases point to scripts that pick the correct executables.
alias jip="$JIP_HOME/bin/jip"
alias xd="$JIP_HOME/bin/display"
alias align="$JIP_HOME/bin/align"
alias glm="$JIP_HOME/bin/glm"
alias rem="$JIP_HOME/bin/rem"

# Using any argument to this script will suppress output.
if [ $# -eq 0 ]
then
echo "Defined JIP_HOME to be $JIP_HOME"
echo "Defined these aliases: jip, xd, align, glm, rem"
fi

Welcome to Open-Discussion

Christian Haselgrove — Fri, 11 Dec 2009 20:07:01 GMT

Welcome to Open-Discussion