The FieldTrip version that we release includes compiled mex files for the most common platforms (Windows, Linux, macOS). However, it might be that you have a combination of operating system and MATLAB on which the precompiled mex files are not included or on which they do not work. In that case you have to (re)compile them yourself.

The source code for the mex files is mostly contained in the fieldtrip/src directory. Some mex files are contained in fieldtrip/external, for example for SPM. Those are not the responsibility of the FieldTrip team.

To (re)compile all mex files at once, you can use the ft_compile_mex function.

You can recompile individual mex files for your platform using the following commands:

cd fieldtrip/src
mex meg_leadfield1.c
mex plgndr.c
mex read_24bit.c

The following files all depend on some shared code in geometry.c and geometry.h, hence the compilation process is slighty different for these:

mex -I. -c geometry.c		
mex -I. -c solid_angle.c ; mex -o solid_angle solid_angle.o geometry.o
mex -I. -c lmoutr.c      ; mex -o lmoutr      lmoutr.o      geometry.o
mex -I. -c ptriproj.c    ; mex -o ptriproj    ptriproj.o    geometry.o
mex -I. -c ltrisect.c    ; mex -o ltrisect    ltrisect.o    geometry.o
mex -I. -c routlm.c      ; mex -o routlm      routlm.o      geometry.o
mex -I. -c plinproj.c    ; mex -o plinproj    plinproj.o    geometry.o

If you are on a Windows computer, the compiled object files with have extension *.obj instead of *.o and hence you then should do

mex -I. -c geometry.c
mex -I. -c solid_angle.c ; mex solid_angle.c solid_angle.obj geometry.obj
mex -I. -c lmoutr.c      ; mex lmoutr.c      lmoutr.obj      geometry.obj
mex -I. -c ptriproj.c    ; mex ptriproj.c    ptriproj.obj    geometry.obj
mex -I. -c ltrisect.c    ; mex ltrisect.c    ltrisect.obj    geometry.obj
mex -I. -c routlm.c      ; mex routlm.c      routlm.obj      geometry.obj
mex -I. -c plinproj.c    ; mex plinproj.c    plinproj.obj    geometry.obj

After compilation the mex files are automatically at the right location.

Note that most of the mex files include a m-file wrapper which will try to do an auto compilation. Again, the autocompilation has not (and can not) be tested on all possible platforms, so your mileage may vary.

If you are using the Visual Studio Compiler and get an error similar to:

error LNK2005: mexFunction already defined in ptriproj.obj

then try this line replacing ptriproj with the file you are trying to compile.

mex -I. -c ptriproj.c    ; mex ptriproj.c  geometry.obj

Note in Linux: If you are get the error message “cannot find -lstdc++”, you can install the libstdc++5 package using your package manager. If, after the install of libtdc++5, the lstdc++ error persists, just do a symbolic link like

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

and it should work.

Some MEX files have been recompiled but have not been tested on all platform combinations with FieldTrip, and hence are not yet included in the current release. Examples thereof are the MEX files provided by external software packages. Below is a list of currently known issues (January, 2018) and their workarounds, other than recompiling the incompatible MEX files yourself.

Producing the following error

Invalid MEX-file '/Users/roboos/matlab/fieldtrip/external/spm8/spm_conv_vol.mexmaci64':
dlopen(/Users/roboos/matlab/fieldtrip/external/spm8/spm_conv_vol.mexmaci64, 6): Library not loaded: @loader_path/libmex.dylib
Referenced from: /Users/roboos/matlab/fieldtrip/external/spm8/spm_conv_vol.mexmaci64
Reason: image not found. 

1) You can recompile the SPM8 mex files. A makefile and instructions are provided on https://www.wikibooks.org/wiki/SPM#Installation.

2) You can use the maintenance version of SPM8 which has newer mex files, see https://github.com/spm/spm8/tree/maint

3) Mex file issues should be resolved using the latest version of SPM12. You can specify the use of SPM12 at function call

cfg.spmversion = 'spm12' or 'spm8up'

4) For a more permanent solution that applies to all functions from the FieldTrip toolbox, you can set SPM12 as the default version in your startup.m

 global ft_default
 ft_default.spmversion = 'spm12'
 ft_defaults % this loads the rest of the defaults

Producing the following error

 Error using read_gifti_file (line 17)
 [GIFTI] Loading of XML file /Users/arjsto/Projects/Ecog/data/IR30/recon/freesurfer/SUMA/std.141.lh.pial.gii failed.

You can replace the xml_findstr.mexmaci64 in external/gifti/@xmltree/private by the version hosted at https://github.com/spm/spm12/blob/master/%40xmltree/private/xml_findstr.mexmaci64