1 Packages for the complete FSL suite
2 ===================================
4 Since FSL covers a very broad range of analysis techniques the suite is split
5 into a number of separate packages to allow a more fine-grained selection of
6 the functionality provided by FSL. The following related packages are available:
9 This packages provides the FSL binaries. This includes everything one needs
10 to run a basic fMRI analysis. However, it is recommend to also at least
11 install the :ref:`fsl-atlases <pkg_fsl-atlases>` package.
14 Almost everybody should install this package.
17 Contains the FSL documentation in HTML format as included in the official FSL
18 sources. This package should be installed to use the online help capabilities
21 :ref:`pkg_fslview-doc`
22 The FSLView documentation in HTML format. This package is necessary for the
23 online help system of FSLView.
25 :ref:`pkg_fsl-atlases`
26 Contains the standard space brain templates and brain atlases. Almost
27 everybody should install this package.
29 :ref:`pkg_fsl-possum-data`
30 This package provides the templates for the MR sequence simulator POSSUM.
31 If one does not use POSSUM this package is not necessary.
33 :ref:`pkg_fsl-first-data`
34 This package provides model data for FIRST subcortical brain segmentation.
35 This package is almost 1GB! It is only required if one wants to use FIRST
36 or run the FSL FEEDS suite.
39 This package provides the `FSL Evaluation and Example Data Suite`_. This
40 package performs two functions -- it tests whether the FSL tools are working
41 properly and it provides example data to try running FSL on. Additionally the
42 :command:`fsl-selftest` command is avaliable. This is a little script that
43 runs all tests (or a selected one) in a temporary directory and reports the
44 results. A manpage is included. This package can be used to perform
47 .. _FSL Evaluation and Example Data Suite: http://www.fmrib.ox.ac.uk/fsl/fsl/feeds.html
53 If you discover any bugs please report them. The best way to get quick and
54 professional help is to post to the `FSL mailing list`_. If you send a
55 bugreport please include detailed information about the problem. This should at
56 least be a description how the bug can be reproduced as well as information
57 concerning you environment (for example the operation system). You might also
58 want to have a look at the mailing list archive whether the problem has been
61 .. _FSL mailing list: http://www.jiscmail.ac.uk/lists/fsl.html
63 If you use the package on a Debian system (not Ubuntu) you can simply use the
64 :command:`reportbug` tool to send a bug report to the `Debian bug tracking
65 system`_. The bug tracker provides a public list of all reported `bugs of FSL`_
66 and `bugs of FSLView`_
68 .. _bugs of FSL: http://bugs.debian.org/src:fsl
69 .. _bugs of FSLVIEW: http://bugs.debian.org/src:fslview
70 .. _Debian bug tracking system: http://bugs.debian.org
73 Additional information
74 ======================
76 Since December 2007 the FSL package is officially part of the non-free
77 section of Debian. The latest package version will always be available
78 from http://packages.debian.org/sid/fsl in the Debian archive.
79 However, this only applies to the packages of the FSL and FSLView
80 binaries. FSL data packages (first, possum, atlases and feeds) are not
81 yet official Debian packages and will be available from here, as well
82 as backports for Debian and recent Ubuntu releases.
86 Please be sure to `read the information`_ about the differences
87 between the Debian packaging and the official FSL releases.
89 .. _read the information: http://git.debian.org/?p=pkg-exppsy/fsl.git;a=blob_plain;f=debian/README.Debian;hb=HEAD
95 FSL requires a config file to be sourced before it can be used. For the Debian
96 packages this config file is in `/etc/fsl/fsl.sh`. Open a terminal where you
97 want to start FSL and source it like this::
101 Note the dot at the beginning. If you want to have this done automatically, you
102 could add those line to e.g. your `$HOME/.bashrc` file (or a corresponding
103 config file of another POSIX-compatible shell). Once you have done that, you
108 Upgrading from FSL 3.x
109 ----------------------
111 The FSL configuration file has changed significantly. Please be sure to
116 There seem to be some remaining incompatibilities of FSL scripts with the
117 *dash* shell. This is the default shell on Ubuntu systems. If you discover any
118 problems, please make sure to read `a related posting on the FSL mailing
121 .. _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
124 Building binary packages yourself
125 ---------------------------------
127 If no binary packages for your distribution/platform are available, you can
128 still build your own. All you need to do is to add this line to your
129 `/etc/apt/sources.list`::
131 deb-src http://apsy.gse.uni-magdeburg.de/debian #distro# main non-free
133 Choose the value of `#distro#` like described in the binary package section. Be
134 sure to update your package list after that (Remember: :command:`aptitude
135 update`). To build FSL packages, do this (no superuser privileges required,
136 but you might have to install `apt-src` first)::
141 Be patient as this will take some time. All packages will be created in the
142 directory where the commands are executed. Please note, that you might need to
143 download or even compile other packages that FSL depends on.
145 If you are done, you can install the packages with::
149 After you have repeated this procedure for the `fslview` source package, you
150 should be ready to use FSL.
152 Advanced: Arch-dependend compiler flags
153 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
155 If you have some experience with compiler flags and you also care for speed,
156 you might want to have the FSL binaries optimized for every detail of your
157 platform. To take advantage of all special features of your favorite processor
158 you can specify custom compiler flags that are used when building binary
159 packages from the source package of FSL. To achieve this, simply define them in
160 a variable called :envvar:`DEB_ARCH_OPT_FLAGS` in the environment. In its
161 simplest form, building an optimized package could be done like this::
163 DEB_ARCH_OPT_FLAGS="-march=opteron" apt-src build fsl
165 Note that not all flags are available with every compiler. The above example
166 does not work with the standard compiler of Debian sarge (gcc 3.3) and you
167 obviously need an AMD Opteron processor.
173 Here is a list of some benchmarking results that demonstrate how fast FSL runs
174 on several different platforms and distributions. The :command:`fsl-feeds`
175 package is used for benchmarking FSL. The listed time for a complete
176 fsl-selftest run is the user time as reported by :command:`time -p`. If you are
177 also interested in benchmarking results of the non-Debian FSL distribution, you
178 can visit the `FSL-FEEDS timing website`_.
180 .. _FSL-FEEDS timing website: http://www.fmrib.ox.ac.uk/fsl/feeds/doc/timings.html
182 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
183 |Distribution|CPU |Arch. |Memory|Compiler |Flags |Version |Time|Submitted |
184 +============+===============+======+======+=========+==================+========+====+==============+
185 |Ubuntu |Intel Core i7 |x86_64|12GB |gcc 4.3 | |4.1.3-1 |1236| Jiří Keller |
186 |jaunty |8 cores 3.4 Ghz| | | | | | | |
187 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
188 |Ubuntu |Intel Core 2 |x86_64|4GB |gcc 4.1.2| |4.0.2-1 |1377| Jiří Keller |
189 |gutsy |Quad Q6700 3Ghz| | | | | | | |
190 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
191 |Debian sid |2x Dual Opteron|amd64 |12GB |gcc 4.1.1| |3.3.7-2 |1560|Yaroslav |
192 | |275 2.2 Ghz | | | | | | |Halchenko |
193 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
194 |Ubuntu edgy |2x Dual Opteron|i686 |3GB |gcc 4.1.2| |3.3.8-1 |2096|Jeff |
195 | |275 2.2 GHz | | | | | | |Stevenson |
196 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
197 |Debian lenny|Intel Core2 |i686 |2GB |gcc 4.3.1| |4.1.0-1 |2108|Michael |
198 | |E8400 3Ghz | | | | | | |Hanke |
199 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
200 |Debian etch |Quad Opteron |amd64 |32GB |gcc 3.4.6|-O3 -m64 |3.2b-4 |2152|Antti |
201 | |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
202 | | | | | |-mfpmath=sse | | | |
203 | | | | | |-msse2 | | | |
204 | | | | | |-ffast-math | | | |
205 | | | | | |-funroll-all-loops| | | |
206 | | | | | |-fpeel-loops | | | |
207 | | | | | |-ftracer | | | |
208 | | | | | |-funswitch-loops | | | |
209 | | | | | |-funit-at-a-time | | | |
210 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
211 |Debian lenny|Athlon X2 |amd64 |4GB |gcc 4.3 | |4.0.4-1 |2268|Petr |
212 | |4800 2.5 GHz | | | | | | |Hluštík |
213 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
214 |Ubuntu |Quad Core2 |amd64 |4GB |gcc 4.1 | |4.0-1 |2500|Vincent |
215 |feisty |2.4 GHz | | | | | | |Ferrera |
216 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
217 |Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 -m64 |3.2b-4 |2619|Antti |
218 | |850 2.4 GHz | | | |-march=opteron | | |Korvenoja |
219 | | | | | |-mfpmath=sse | | | |
220 | | | | | |-msse2 | | | |
221 | | | | | |-ffast-math | | | |
222 | | | | | |-funroll-all-loops| | | |
223 | | | | | |-fpeel-loops | | | |
224 | | | | | |-ftracer | | | |
225 | | | | | |-funswitch-loops | | | |
226 | | | | | |-funit-at-a-time | | | |
227 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
228 |Debian etch |Quad Opteron |amd64 |32GB |gcc 4.0.2|-O3 |3.2b-4 |2652|Antti |
229 | |850 2.4 GHz | | | | | | |Korvenoja |
230 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
231 |Debian etch |2x Opteron |amd64 |12GB |gcc 4.1.2| |4.0.2-3 |2847|Michael |
232 | |270 2.2 GHz | | | | | | |Hanke |
233 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
234 |Ubuntu gutsy|Athlon 64X2 |amd64 |2GB |gcc 4.1.3| |4.0.1 |3605|Nicholas P. |
235 | |5200+ 2.6 GHz | | | | | | |Holmes |
236 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
241 +------------+---------------+------+------+---------+------------------+--------+----+--------------+
244 If you want to have your system included in this list, please send an email
245 with the logfile of the benchmark. You can run the benchmark (and create the
246 logfile) by running (fsl-feeds-3.2beta-3 or higher is required)::
248 (time -p fsl-selftest -c) > benchmark.log 2>&1
250 And include the following information in your message:
252 * Which distribution are you using?
254 * CPU-type (as specific as possible)
256 * How much physical memory has the machine? If you don't know this, send the
259 free | head -n2 | tail -n1 | awk '{print $2}' -
261 * If you compiled the binary packages yourself, which compiler did you use?
262 (hint: `gcc --version`)
264 * Which custom compiler flags did you use when building the package (if any)?
266 * Which version of the Debian FSL package was used?