First, I installed Fedora 13 using installation DVD made myself. (The content is downloaded from http://fedoraproject.org/) The procedure is quite straightforward. Follow the instruction on the screen. The system was successfully installed.
Second, I installed AFNI using following steps (adapted from AFNI website).
Step 0: enter these commands to prepare for the installation:
cd
mkdir abin
The first command, 'cd', is used just to make sure the user is in
their home directory, before issuing further commands.
The second command, 'mkdir abin' is used to create the directory
which will be used to store the actual programs from the AFNI
package. The main reason that 'abin' (for "AFNI binaries") is
chosen for a name is to allow the descriptions to be more generic,
and less dependent upon which operating system is in use.
Step 1: enter these commands to get and unpack the AFNI binary package:
wget http://afni.nimh.nih.gov/pub/dist/tgz/linux_gcc32.tgz
tar xvfz linux_gcc32.tgz
mv linux_gcc32/* abin
rmdir linux_gcc32
The first command, 'wget http://...' is used to actually download
the AFNI package. The user may use their browser, pointed to
pub/dist/tgz to find the linux_gcc32.tgz package, also.
The second command, 'tar xvfz linux_gcc32.tgz' is used to
extract the contents (the programs) of the compressed package.
The options used with this tar command are:
x - to extract the contents of the archive
v - verbose, to display files as they are extracted
f - file, the next argument is the tar file to expand
z - uncompress the file before extracting its contents
See 'man tar' for more details.
The third command, 'mv linux_gcc32/* abin' moves everything from
the newly extracted linux_gcc32 directory into the abin directory.
The final command, 'rmdir linux_gcc32' is used to remove the
empty linux_gcc32 directory, now that its contents have been
moved to abin.
Note: this linux_gcc32.tgz package includes SUMA.
Step 2: enter these commands to get and unpack some sample data:
wget http://afni.nimh.nih.gov/pub/dist/edu/data/AFNI_data1.tgz
tar xvfz AFNI_data1.tgz
The first command, 'wget http://...' is used to download the
AFNI_data1.tgz sample data package. This package contains
SPGR anatomy, EPI time-series data, and an 'afni' directory,
with datasets made from that raw data. The user may also use
their browser to download AFNI_data1.tgz.
The 'tar xvfz ...' command is to extract the AFNI_data1
directory from the compressed archive. The tar options are
the same as in Step 1.
Step 3: enter this command to add the directory ~/abin to your PATH:
gedit ~/.bash_profile
Then you will see a file open and change it to the following contents:
# .bash_profile
# Get the aliases and functions
if [ -f ~/.bashrc ]; then
. ~/.bashrc
fi
# User specific environment and startup programs
PATH=$PATH:$HOME/abin
export PATH
Save it.
Step 4: log out and log back in
This is done to invoke the change to the .cshrc file, meaning
that any new terminal window would have a command shell with
~/abin in the PATH. It also has the effect of using the
'rehash' command, which tells the shell (T-shell) to make note
of all executables in the PATH.
Step 5: open a new terminal window, and start playing!
cd AFNI_data1/afni
afni
Note that if the 'afni' command fails, you may want to review the
steps that have been taken. There are two commands that may help
resolve any problems:
echo $PATH
It worked. You might need to install netpbm rpm packages for supporting different image formats. (warning message might look like this)
Initializing: X11.
++++++++ IMAGE SAVE SETUP WARNINGS ++++++++
++ Can't find program ppmtogif AND/OR ppmquant for Save to GIF
++ Can't find program ppm2tiff OR pnmtotiff for Save to TIFF
++ Can't find program ppmtobmp for Save to BMP
++ Can't find program pnmtops for Save to EPS
++ Can't find program pnmtopng for Save to PNG
++ Some of the missing image Save programs are in
++ the netpbm software package, which is freeware.
++ Netpbm can be found at http://netpbm.sourceforge.net/
++ To disable these warnings, set environment
++ variable AFNI_IMSAVE_WARNINGS to 'NO'.
+++++++++++++++++++++++++++++++++++++++++++
Third, I installed CTF software package.
[root@localhost Downloads]# mkdir /tmp/mnt
[root@localhost Downloads]# mount -o loop,ro -t iso9660 ctf-5.4.0CD_20061212.iso /tmp/mnt
[root@localhost Downloads]# cd /tmp/mnt
[root@localhost mnt]# ./CTF.install
(c) Copyright VSM MedTech Ltd. All Rights Reserved.
Description:
This script updates or installs the CTF_MEG MEG/EEG Software suite.
If a current installation is not found, then a "complete install" is performed
otherwise, an upgrade is performed. An upgrade copies all executable and script
files from the distribution CD-ROM to the CTF_MEG software directory.
The CTF.install will then copy any configuration files that are on the CD-ROM
but are missing in the CTF_MEG directory. The user is given the option of
copying all configuration files, as well as creating backups of all
existing files that are over written.
If necessary, CTF.install will install acroread ( PDF file reader ) and
openmotif, ghostscript, Python, Xdialog, Xprint, a set of pixmap conversion
programs, and a set of postscript conversion programs.
Checking current installation....
The directory /opt/ctf does not exist
Is this a new installation? [
Please enter a destination path for the installation? [
Please enter path of the source directory for the install? [ ]/tmp/mnt
Select which electronics system is in use.
CTF_MEG2000 -- Contains DSQ-2041/DSQ-2043 DSP bank with DSQ-2010 SQUID Channel Units
and rack mounted ADC/Trigger units
CTF_MEG2005 -- Contains DSQ-2041/DSQ-2043 based DSP bank with DSQ-2010 SQUID Channel Units
and desktop Electronic Control Console
Select "Skip" to skip installation of electronics specific files.
1) CTF_MEG2000
2) CTF_MEG2005
3) Skip
Select electronics system version :3
Checking for required libraries ...
Dynamically shared library file libXm.so.3 needed by CTF software is missing
Please insure that you are installing the software on RedHat Enterprise 3.0 or higher
Installation of the CTF_MEG MEG/EEG Software has failed prematurely.
Do you want to continue [ y,
solve libXm.so.3 problem:
#cd /usr/lib
#ln -s libXm.so.4 libXm.so.3
Then you will get another error: libstdc++.so.5
#yum install compat-libstdc++-33-3.2.3-68.i686
Reference: http://kurage.nimh.nih.gov/meglab/Meg/CTFSoftwareInstallation
If you have specific problems, feel free to contact me.
openmotif is the key package which has to be installed properly. :)
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