I am trying to run spm12 with matlab 2023b on my macOS but I got this error when I type spm and I have already installed xcode14 from App Store

>> spm

Error using spm_check_installation>check_basic

SPM uses a number of MEX files, which are compiled functions.

These need to be compiled for the various platforms on which SPM

is run. It seems that the compiled files for your computer platform

are missing or not compatible. See

https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)

for information about how to compile MEX files for MACA64

in MATLAB 23.2.0.2391609 (R2023b) Update 2.

[Walter Roberson]

See https://www.mathworks.com/matlabcentral/answers/2021036-matlab-is-not-running-spm12-on-r2023b#answer_1312707 -- but I am not convinced it will work.

[NADA]

>> mex -setup

MEX configured to use 'Xcode with Clang' for C language compilation.

To choose a different language, select one from the following:

mex -setup C++

mex -setup FORTRAN

>>

[NADA]

after typing >> mex -setup on matlab window commands i see this

>> mex -setup

MEX configured to use 'Xcode with Clang' for C language compilation.

To choose a different language, select one from the following:

mex -setup C++

mex -setup FORTRAN

>>

[Walter Roberson]

That is fine, but the link I posted for you has to do with Apple's security mechanisms. The files might have been compiled but MacOS might be refusing to pay attention to them for security reasons.

[NADA]

i tried the link you gave to me

it says Permission denied

[Walter Roberson]

The command

sudo spctl --master-disable

should be run in the Terminal utility -- or at the MATLAB command line you can command

!sudo spctl --master-disable

with the leading exclamation mark.

This will prompt you for your password. If the administor of your system has configured your account to be permitted enhanced access then MacOS will permit the command to e executed.

If you do not have access to an administrator account on the Apple Silicon system then you will need to get an administrator to execute the command.

[NADA]

okay i wrote it and

what should i do after that ?

[Walter Roberson]

After that, it might start working, or perhaps it will work if you reinstall after that.

[Ruben Krueger]

Hello, I am having this same issue, and the above answer does not work for me. Here's my system:

- Apple M1 Sonoma

- Matlab 2023b

Answer 1

[Laurent Lamalle]

Hello,

Look first at: https://en.wikibooks.org/wiki/SPM/Installation_on_64bit_Mac_OS_(Intel)

For SPM12, on my M2-based PowerBook Pro, I succeeded compiling mexmaca64 mex files using the following procedure:

• In spm12/src, I edited "Makefile.var" and replaced "mexmaci64" with "mexmaca64" in the MacOS section:
• ##### MacOS #####
• ifeq (Darwin,$(PLATFORM))
• MEXEXT = mexmaca64
• ...
• In spm12/src, I edited "Makefile" and added in the "Display Messages" section a line to handle mexmaca64:
• verb.mexmaci64:
• $(call verb, "MacOS compilation (Intel 64 bit)")
• verb.mexmaca64:
• $(call verb, "MacOS compilation (ARM 64 bit)")
• After that, the commands "make" and "make install" both run successfully (current directory being spm12/src).
• I edited spm12/external/src/geometry.c, to add:
• #include "mex.h"
• after #include "geometry.h".
• Then, the command:
• CFLAGS="-I/PathTo/MATLAB_R2023b.app//extern/include/" make external
• succeeds, as well as
• make external-install.
• I further edited spm12/spm_platform.m to insert the line:
• 'MACA64', 'unx', 0;...
• after the line
• 'MACI64', 'unx', 0;...
• and changed
• case {'MAC','MACI','MACI64'}
• to
• case {'MAC','MACI','MACI64','MACA64'}
• in the switch comp cases.

It should be easy to further adapt so that both mexmaci64 and mexmaca64 could be compiled depending on the CPU architecture underlying the particular Darwin platform.

Now, it seems that the developer version of SPM (on github.com) includes already mexmaca64 files...

[Lorenzo]

Hi! Thank you very much for your answer. I am trying to install SPM12; while the developer version works fine, I have problem following this solution. Once I have Makefile (line 11), if I run make && make install i got this message:

mex -O -largeArrayDims -c spm_vol_utils.c -DSPM_UNSIGNED_CHAR 
make: mex: No such file or directory
make: *** [utils_uchar.mexmaca64.o] Error 1

Unfortunately, the dev version does not work with brainageR, which is the reason I am trying to install SPM.

Do you have any suggestion? I am running on a mac mini M2, Sonoma.

Thank you

[Lorenzo]

Apparently resolved downloading again SPM.

[Xiaoqing]

hello, I met the same issue. I did as the steps mentioned above.

But at the step make && make install step, I got this message:

cp -f spm_sample_vol.mexmaca64 spm_slice_vol.mexmaca64 spm_brainwarp.mexmaca64 spm_conv_vol.mexmaca64 spm_render_vol.mexmaca64 spm_global.mexmaca64 spm_resels_vol.mexmaca64 spm_bsplinc.mexmaca64 spm_bsplins.mexmaca64 spm_unlink.mexmaca64 spm_existfile.mexmaca64 spm_gamrnd.mexmaca64 spm_hist.mexmaca64 spm_krutil.mexmaca64 spm_project.mexmaca64 spm_hist2.mexmaca64 spm_dilate_erode.mexmaca64 spm_bwlabel.mexmaca64 spm_get_lm.mexmaca64 spm_voronoi.mexmaca64 spm_mesh_dist.mexmaca64 spm_mesh_utils.mexmaca64 spm_mrf.mexmaca64 spm_diffeo.mexmaca64 spm_field.mexmaca64 spm_cat.mexmaca64 spm_jsonread.mexmaca64 spm_mesh_reduce.mexmaca64 spm_mesh_geodesic.mexmaca64 spm_mesh_ray_triangle.mexmaca64 spm_gmmlib.mexmaca64 ..

cp: spm_sample_vol.mexmaca64: No such file or directory

cp: spm_slice_vol.mexmaca64: No such file or directory

cp: spm_brainwarp.mexmaca64: No such file or directory

cp: spm_conv_vol.mexmaca64: No such file or directory

cp: spm_render_vol.mexmaca64: No such file or directory

cp: spm_global.mexmaca64: No such file or directory

cp: spm_resels_vol.mexmaca64: No such file or directory

cp: spm_bsplinc.mexmaca64: No such file or directory

cp: spm_bsplins.mexmaca64: No such file or directory

cp: spm_unlink.mexmaca64: No such file or directory

cp: spm_existfile.mexmaca64: No such file or directory

cp: spm_gamrnd.mexmaca64: No such file or directory

cp: spm_hist.mexmaca64: No such file or directory

cp: spm_krutil.mexmaca64: No such file or directory

cp: spm_project.mexmaca64: No such file or directory

cp: spm_hist2.mexmaca64: No such file or directory

cp: spm_dilate_erode.mexmaca64: No such file or directory

cp: spm_bwlabel.mexmaca64: No such file or directory

cp: spm_get_lm.mexmaca64: No such file or directory

cp: spm_voronoi.mexmaca64: No such file or directory

cp: spm_mesh_dist.mexmaca64: No such file or directory

cp: spm_mesh_utils.mexmaca64: No such file or directory

cp: spm_mrf.mexmaca64: No such file or directory

cp: spm_diffeo.mexmaca64: No such file or directory

cp: spm_field.mexmaca64: No such file or directory

cp: spm_cat.mexmaca64: No such file or directory

cp: spm_jsonread.mexmaca64: No such file or directory

cp: spm_mesh_reduce.mexmaca64: No such file or directory

cp: spm_mesh_geodesic.mexmaca64: No such file or directory

cp: spm_mesh_ray_triangle.mexmaca64: No such file or directory

cp: spm_gmmlib.mexmaca64: No such file or directory

make: *** [main-install] Error 1

I tried download the dev version spm again, but it still failed.

Do you have any suggestion, here is my system.

Apple M2 Sonoma

[Stefan Möller]

I had similar issues as NADA and Lorenzo. What worked for me was doing the changes to Makefile and Makefile.var as Laurent suggested. In Makefile.var I also changed MEXBIN to

MEXBIN = /Applications/MATLAB_R2023b.app/bin/mex

and in this line

MEXOPTS      = -O -largeArrayDims

I changed the "-" because it might have gotten misread by the system. I don't know if that changed anythong though.

I then changed MACI64 to MACA64 in a few places in spm_platform to get SPM to start.

Answer 2

[Amir Dehsarvi]

Just install SPM12 the developers version.

[Cynthia]

Great!!!!