SPM/Installation on 64bit Linux

All versions of SPM are supported under Linux 64 bit and the installation should be fairly the same with any version. You might have to recompile SPM MEX files (*.mexa64) if those provided with the SPM distribution do not appear to be compatible with your system.

SPM12

Installation

Download spm12.zip and its updates spm12_updates_rxxxx.zip in your home directory then type the following in a Terminal:

cd /home/login
unzip spm12.zip
unzip -o spm12_updates_rxxxx.zip -d spm12

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /home/login/spm12

in MATLAB's workspace.

Compilation

In a Terminal, from the src folder of your SPM12 installation, type:

cd /home/login/spm12/src
make distclean
make && make install
make external-distclean
make external && make external-install

SPM8

Installation

Download spm8.zip and its updates spm8_updates_rxxxx.zip in your home directory then type the following in a Terminal:

cd /home/login
unzip spm8.zip
unzip -o spm8_updates_rxxxx.zip -d spm8

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /home/login/spm8

in MATLAB's workspace.

Compilation

In a Terminal, from the src folder of your SPM8 installation, type:

cd /home/login/spm8/src
make distclean
make && make install
make toolbox-distclean
make toolbox && make toolbox-install
make external-distclean
make external && make external-install

Required development packages: make, gcc.

If you get an error message regarding "ft_getopt" then please download a maintenance version of SPM8 and skip the compilation steps above entirely. All the necessary files including mex files for windows, linux and mac should be already compiled. This distribution gives compile time error for nanmean.c though. (ref: https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=spm;9d67787a.1802)

SPM5

Installation

Download spm5.zip and its updated MEX files SPM5_Matlab7.9_LINUX64_MEX.zip in your home directory then type the following in a Terminal:

cd /home/login
unzip spm5.zip
unzip -o SPM5_Matlab7.9_LINUX64_MEX.zip -d spm5

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /home/login/spm5

in MATLAB's workspace.

Compilation

In a Terminal, from the src folder of your SPM5 installation, type:

cd /home/login/spm5/src
make distclean
make && make install

If you receive the following error message: mex: link of ' "spm_bwlabel.mexa64"' failed, then edit spm_bwlabel.c at line 364 such that it reads:

   plhs[1] = mxCreateDoubleScalar(nl);

Ref: McGeown, William. "Re: mex files SPM5 64bit," JISCMail. 13 Apr 2015. Last Accessed 18 Sep 2018.

SPM2

Installation

Download spm2.tar.gz and its updated MEX files SPM2_LINUX64_MEX.tar.gz in your home directory then type the following in a Terminal:

cd /home/login
tar xvfz spm2.tar.gz
tar xvfz SPM2_LINUX64_MEX.tar.gz -C spm2

Start MATLAB and add SPM into your path, either using File > Set Path > Add Folder... or typing

addpath /Users/login/spm2

in MATLAB's workspace.

Compilation

In a Terminal, type:

cd /home/login/spm2
make clean.Linux.A64
make Linux.A64

Troubleshooting

"bad image handle dimensions" error

The error "bad image handle dimensions" when trying to display an image is an indication that you need to (re)compile the SPM MEX files.

"cannot find -lstdc++" error

If you get the error message "cannot find -lstdc++", try installing the build-essential package using your package manager (i.e. sudo apt-get install build-essential on Ubuntu), or the specific libstdc++5 package (replacing 5 with the version of your system) with sudo apt-get install libstdc++5.

If, after the install of libstdc++5, the lstdc++ error persists, just add a symbolic link with:

sudo ln -s /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so 

and it should work. If not, see next.

For old versions of Ubuntu and MATLAB, have a look at these instructions.

Other problems with lstdc++

If you get the above error and cannot install libstdc++ (e.g. you do not have root/admin access), or if you get other problems such as "... version `GCC_4.2.0' not found (required by /usr/lib64/libstdc++.so.6", then another option is to edit your mexopts.sh config file and delete or disable the -lstdc++ compiler flags, for example simply use find-and-replace to delete all instances of -lstdc++. SPM will compile properly without this.

It's best to edit a local copy of mexopts.sh (the original is found in the bin directory with your matlab and mex executables). If you run mex -setup it will interactively create a copy for you, under ~/.matlab/RELEASE for example

~/.matlab/R14SP3/mexopts.sh
~/.matlab/R2008b/mexopts.sh

or similar, and you may then further edit that copy if required. If you match the release, mex will find your copy of mexopts.sh. Note that from MATLAB

version

should show you the release, but with parentheses around it, e.g. "(R14SP3)".

"mex: command not found" error

If you get the error "mex: command not found" check that mex is in your path. Either add the MATLAB binary directory (usually /usr/local/matlab/bin) to your path or create a link to mex somewhere already in the path (usually /usr/local/bin).

• Adding the path:
  • Type: PATH=/usr/local/matlab/bin:$PATH
• Creating a Link:
  • Enter your local binary direcotry: cd /usr/local/bin
  • Create the link: ln -s /usr/local/matlab/bin/mex
  • (Note: Creating a link in /usr/local/bin requires root privileges).

Another solution is to edit the Makefile (spm8/src/Makefile.var for SPM8 or spm5/src/Makefile for SPM5) and mention the full path when referring to MEXBIN:

MEXBIN = /usr/local/matlab/mex

"This is pdfTeX, Version ... (TeX Live 2011)" error

If you get the error:

mex: unrecognized option `-O'
mex: unrecognized option `-c'
This is pdfTeX, Version ... (TeX Live 2011)

This is due to a conflict between MATLAB mex and a LaTeX command (from the texlive package) with the same name. Change PATH or MEXBIN as described in the previous solution.

Missing files

If you get build errors such as math.h does not exist when trying to execute the command "make && make install", then you probably need to install the build-essentials package. At the command line type: "sudo aptitude install build-essential" (for Ubuntu). if you have sudo privileges or simply log in as root or obtain superuser status and type: "aptitude install build-essential".

"plugin needed to handle lto object" error

Edit spm12/src/Makefile.var at the line defining AR so that it reads:

AR           = gcc-ar rcs

Crash at startup

The following concerns a situation where MATLAB segfaults when opening the SPM interface with errors like "'BadWindow (invalid Window parameter)", "serial 20133 error_code 3 request_code 20 minor_code 0", "Pango-CRITICAL **: pango_font_description_from_string: assertion 'str != NULL' failed", "GLib-CRITICAL **: g_once_init_leave: assertion 'result != 0' failed", "GLib-GObject-CRITICAL **: g_type_register_dynamic: assertion 'parent_type > 0' failed"

This is likely to be an issue with the display of the welcoming message in the Graphics window as a web document.

One fix is to comment one line in spm.m: https://github.com/spm/spm12/blob/r7771/spm.m#L352

Another fix not requiring to modify the SPM source code is to define an environment variable, see: https://github.com/spm/spm12/blob/r7771/spm_browser.m#L54

setenv('SPM_HTML_BROWSER','0')

Compilation notes for SPM2:

Updates for Makefile

In order to make the recompilation process work, the Makefile provided in the spm2.tar.gz package needs to be patched. Also the file spm_platform.m needs an update.

The updated Makefile adds a new architecture, Linux.a64:

Linux.a64:

  make all SUF=mexa64  CC="gcc -O3 -funroll-loops -fPIC -march=x86-64" \

  MEX="mex COPTIMFLAGS='-O3 -funroll-loops -fPIC -march=x86-64'"

Plus an appropriate section for clean and verb.mexa64.

The -fPIC option is necessary to allow linking on 64bit Linux.
-march=x86-64 provides generic optimisations for both Opteron and 64bit Xeon. If the code is running on a 64bit Xeon you can change it to -march=nocona (the first revision of the Xeon processor supporting EM64T had codename nocona), if you have an Opteron or Athlon64, change it to -march=opteron. This might give you an extra performance boost.

Updates for spm_platform.m

Matlab for 64bit Linux identifies itself as GLNXA64 as opposed to GLNX86 when running 32bit Matlab. Endian-ness doesn't change, so I added this to the PDefs cell list:

                'GLNXA64',      'unx',  0;...

and added GLNXA64 to the list of other unix platforms at the font configuration.