MATLAB complains about a missing or invalid mex file, what should I do?
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 recompile them yourself.
The source code for the FieldTrip 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.
Note that in general the toolboxes in
fieldtrip/external are not maintained by the FieldTrip team, but come from an external source.
If you run into problems with mex files from SPM, i.e. the ones included in
fieldtrip/external/spmX, you should have a look at https://en.wikibooks.org/wiki/SPM/MATLAB. See also further down on this page.
Recommended way of recompiling
To recompile all mex files at once, you can use the ft_compile_mex function.
Alternative way of recompiling
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 this
ln -s /usr/lib64/libstdc++.so.6 /usr/lib64/libstdc++.so
and it should work.
Known issues with SPM mex files and workarounds
Some mex files have been compiled but have not been tested by the FieldTrip developpers on all current platforms that we support. Examples are the mex files provided by external software packages. Below is a list of known issues and alternative workarounds, other than recompiling the incompatible mex files yourself.
SPM8 mexmaci64 mex files fail on MATLAB 2017 and up
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.
You can recompile the SPM8 mex files. A makefile and instructions are provided on https://www.wikibooks.org/wiki/SPM#Installation.
You can use the maintenance version of SPM8, which has newer mex files, see https://github.com/spm/spm8/tree/maint.
Most mex file issues are resolved using the latest version of SPM12. You can specify the use of SPM12 with
cfg.spmversion = 'spm12'
For a more permanent solution that applies to all functions from the FieldTrip toolbox, you can set SPM12 as the default version in your
global ft_default ft_default.spmversion = ‘spm12’ ft_defaults % this loads the rest of the defaults, the existing ft_default fields will not be touched
GIFTI mexmaci64 mex file on MATLAB 2017 and up
When you get 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
external/gifti/@xmltree/private by the version from https://github.com/spm/spm12/blob/master/%40xmltree/private/xml_findstr.mexmaci64.