--- /dev/null
+Related packages
+================
+
+Since FSL covers a very broad range of analysis techniques the suite is split
+into a number of separate packages to allow a more fine-grained selection of
+the functionality provided by FSL. The following related packages are available:
+
+:ref:`deb_fsl`
+ This packages provides the FSL binaries. This includes everything one needs
+ to run a basic fMRI analysis. However, it is recommend to also at least
+ install the :ref:`fsl-atlases <deb_fsl-atlases>` package.
+
+:ref:`deb_fslview`
+ Almost everybody should install this package.
+
+:ref:`deb_fsl-doc`
+ Contains the FSL documentation in HTML format as included in the official FSL
+ sources. This package should be installed to use the online help capabilities
+ of FSL.
+
+:ref:`deb_fslview-doc`
+ The FSLView documentation in HTML format. This package is necessary for the
+ online help system of FSLView.
+
+:ref:`deb_fsl-atlases`
+ Contains the standard space brain templates and brain atlases. Almost
+ everybody should install this package.
+
+:ref:`deb_fsl-possum-data`
+ This package provides the templates for the MR sequence simulator POSSUM.
+ If one does not use POSSUM this package is not necessary.
+
+:ref:`deb_fsl-first-data`
+ This package provides model data for FIRST subcortical brain segmentation.
+ This package is almost 1GB! It is only required if one wants to use FIRST
+ or run the FSL FEEDS suite.
+
+:ref:`deb_fsl-feeds`
+ This package provides the `FSL Evaluation and Example Data Suite`_. This
+ package performs two functions -- it tests whether the FSL tools are working
+ properly and it provides example data to try running FSL on. Additionally the
+ :command:`fsl-selftest` command is avaliable. This is a little script that
+ runs all tests (or a selected one) in a temporary directory and reports the
+ results. A manpage is included. This package can be used to perform
+ `FSL benchmarks`_.
+
+.. _FSL Evaluation and Example Data Suite: http://www.fmrib.ox.ac.uk/fsl/fsl/feeds.html
+
+
+Report bugs
+===========
+
+If you discover any bugs please report them. The best way to get quick and
+professional help is to post to the `FSL mailing list`_. If you send a
+bugreport please include detailed information about the problem. This should at
+least be a description how the bug can be reproduced as well as information
+concerning you environment (for example the operation system). You might also
+want to have a look at the mailing list archive whether the problem has been
+discovered before.
+
+.. _FSL mailing list: http://www.jiscmail.ac.uk/lists/fsl.html
+
+If you use the package on a Debian system (not Ubuntu) you can simply use the
+:command:`reportbug` tool to send a bug report to the `Debian bug tracking
+system`_. The bug tracker provides a public list of all reported `bugs of FSL`_
+and `bugs of FSLView`_
+
+.. _bugs of FSL: http://bugs.debian.org/src:fsl
+.. _bugs of FSLVIEW: http://bugs.debian.org/src:fslview
+.. _Debian bug tracking system: http://bugs.debian.org
+
+
+Additional information
+======================
+
+Since December 2007 the FSL package is officially part of the non-free
+section of Debian. The latest package version will always be available
+from http://packages.debian.org/sid/fsl in the Debian archive.
+However, this only applies to the packages of the FSL and FSLView
+binaries. FSL data packages (first, possum, atlases and feeds) are not
+yet official Debian packages and will be available from here, as well
+as backports for Debian and recent Ubuntu releases.
+
+.. note::
+
+ Please be sure to `read the information`_ about the differences
+ between the Debian packaging and the official FSL releases.
+
+.. _read the information: http://git.debian.org/?p=pkg-exppsy/fsl.git;a=blob;f=debian/README.Debian;hb=debian"
+
+
+Usage information
+-----------------
+
+FSL requires a config file to be sourced before it can be used. For the Debian
+packages this config file is in `/etc/fsl/fsl.sh`. Open a terminal where you
+want to start FSL and source it like this::
+
+ . /etc/fsl/fsl.sh
+
+Note the dot at the beginning. If you want to have this done automatically, you
+could add those line to e.g. your `$HOME/.bashrc` file (or a corresponding
+config file of another POSIX-compatible shell). Once you have done that, you
+can start using FSL.
+
+
+
+Upgrading from FSL 3.x
+----------------------
+
+The FSL configuration file has changed significantly. Please be sure to
+(re)source it.
+
+.. note::
+
+ There seem to be some remaining incompatibilities of FSL scripts with the
+ *dash* shell. This is the default shell on Ubuntu systems. If you discover any
+ problems, please make sure to read `a related posting on the FSL mailing
+ list`_.
+
+.. _a related posting on the FSL mailing list: http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0709&L=fsl&T=0&F=&S=&P=19638
+
+
+Building binary packages yourself
+---------------------------------
+
+If no binary packages for your distribution/platform are available, you can
+still build your own. All you need to do is to add this line to your
+`/etc/apt/sources.list`::
+
+ deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# main non-free
+
+Choose the value of `#distro#` like described in the binary package section. Be
+sure to update your package list after that (Remember: :command:`aptitude
+update`). To build FSL packages, do this (no superuser privileges required,
+but you might have to install `apt-src` first)::
+
+ apt-src install fsl
+ apt-src build fsl
+
+Be patient as this will take some time. All packages will be created in the
+directory where the commands are executed. Please note, that you might need to
+download or even compile other packages that FSL depends on.
+
+If you are done, you can install the packages with::
+
+ dpkg -i fsl*.deb
+
+After you have repeated this procedure for the `fslview` source package, you
+should be ready to use FSL.
+
+Advanced: Arch-dependend compiler flags
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+If you have some experience with compiler flags and you also care for speed,
+you might want to have the FSL binaries optimized for every detail of your
+platform. To take advantage of all special features of your favorite processor
+you can specify custom compiler flags that are used when building binary
+packages from the source package of FSL. To achieve this, simply define them in
+a variable called :envvar:`DEB_ARCH_OPT_FLAGS` in the environment. In its
+simplest form, building an optimized package could be done like this::
+
+ DEB_ARCH_OPT_FLAGS="-march=opteron" apt-src build fsl
+
+Note that not all flags are available with every compiler. The above example
+does not work with the standard compiler of Debian sarge (gcc 3.3) and you
+obviously need an AMD Opteron processor.
+
+
+FSL benchmarks
+--------------
+
+Here is a list of some benchmarking results that demonstrate how fast FSL runs
+on several different platforms and distributions. The :command:`fsl-feeds`
+package is used for benchmarking FSL. The listed time for a complete
+fsl-selftest run is the user time as reported by :command:`time -p`. If you are
+also interested in benchmarking results of the non-Debian FSL distribution, you
+can visit the `FSL-FEEDS timing website`_.
+
+.. _FSL-FEEDS timing website: http://www.fmrib.ox.ac.uk/fsl/feeds/doc/timings.html
+
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Distribution|CPU |Arch. |Memory|Compiler |Flags |Version |Time|Submitted |
++============+===============+======+======+=========+==================+========+====+==============+
+|Ubuntu |Intel Core 2 |x86_64|4GB |gcc 4.1.2| |4.0.2-1 |1377| Jiří Keller |
+|gutsy |Quad Q6700 3Ghz| | | | | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian sid |2x Dual Opteron|amd64 |12GB |gcc 4.1.1| |3.3.7-2 |1560|Yaroslav |
+| |275 2.2 Ghz | | | | | | |Halchenko |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu edgy |2x Dual Opteron|i686 |3GB |gcc 4.1.2| |3.3.8-1 |2096|Jeff |
+| |275 2.2 GHz | | | | | | |Stevenson |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian lenny|Intel Core2 |i686 |2GB |gcc 4.3.1| |4.1.0-1 |2108|Michael |
+| |E8400 3Ghz | | | | | | |Hanke |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 3.4.6|-O3 -m64 |3.2b-4 |2152|Antti |
+| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
+| | | | | |-mfpmath=sse | | | |
+| | | | | |-msse2 | | | |
+| | | | | |-ffast-math | | | |
+| | | | | |-funroll-all-loops| | | |
+| | | | | |-fpeel-loops | | | |
+| | | | | |-ftracer | | | |
+| | | | | |-funswitch-loops | | | |
+| | | | | |-funit-at-a-time | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian lenny|Athlon X2 |amd64 |4GB |gcc 4.3 | |4.0.4-1 |2268|Petr |
+| |4800 2.5 GHz | | | | | | |Hluštík |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu |Quad Core2 |amd64 |4GB |gcc 4.1 | |4.0-1 |2500|Vincent |
+|feisty |2.4 GHz | | | | | | |Ferrera |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 -m64 |3.2b-4 |2619|Antti |
+| |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
+| | | | | |-mfpmath=sse | | | |
+| | | | | |-msse2 | | | |
+| | | | | |-ffast-math | | | |
+| | | | | |-funroll-all-loops| | | |
+| | | | | |-fpeel-loops | | | |
+| | | | | |-ftracer | | | |
+| | | | | |-funswitch-loops | | | |
+| | | | | |-funit-at-a-time | | | |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 |3.2b-4 |2652|Antti |
+| |850 2.4 GHz | | | | | | |Korvenoja |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Debian etch |2x Opteron |amd64 |12GB |gcc 4.1.2| |4.0.2-3 |2847|Michael |
+| |270 2.2 GHz | | | | | | |Hanke |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+|Ubuntu gutsy|Athlon 64X2 |amd64 |2GB |gcc 4.1.3| |4.0.1 |3605|Nicholas P. |
+| |5200+ 2.6 GHz | | | | | | |Holmes |
++------------+---------------+------+------+---------+------------------+--------+----+--------------+
+
+.. Template
+ | | | | | | | | | |
+ | | | | | | | | | |
+ +------------+---------------+------+------+---------+------------------+--------+----+--------------+
+
+
+If you want to have your system included in this list, please send an email
+with the logfile of the benchmark. You can run the benchmark (and create the
+logfile) by running (fsl-feeds-3.2beta-3 or higher is required)::
+
+ (time -p fsl-selftest -c) > benchmark.log 2>&1
+
+And include the following information in your message:
+
+* Which distribution are you using?
+
+* CPU-type (as specific as possible)
+
+* How much physical memory has the machine? If you don't know this, send the
+ output of::
+
+ free | head -n2 | tail -n1 | awk '{print $2}' -
+
+* If you compiled the binary packages yourself, which compiler did you use?
+ (hint: `gcc --version`)
+
+* Which custom compiler flags did you use when building the package (if any)?
+
+* Which version of the Debian FSL package was used?
projects / neurodebian.git / blobdiff