Segmentation fault during OpenMEEG head model calculation

lerud · August 13, 2018, 11:28pm

Hello. I've got T1 images, BESA EEG sensor coordinates, and EEG data from several individual subjects. I have segmented all the MRIs with FreeSurfer and imported them into Brainstorm. I have also imported all the individual BESA coordinates into Brainstorm. I am now starting to construct head models for the individual subjects. My source model consists of ~15,000 vertices of neocortex, as well as a volume composed of some subcortical structures.

On Ubuntu: After starting "Compute head model", it runs for about 24 minutes, gets to the point where the dialog says "Assembling EEG leadfield", then the process crashes with the attached segmentation fault error. I tried it with several different subjects, and the same thing happens every time.

On macOS: The head models finish successfully to completion in about 32 minutes, identical data.

I'm using the mac laptop for now, but my Ubuntu machine is more powerful so I'd prefer to use that, so I am wondering if there is anything that can be done about this error, on my end or yours. I will probably need to provide more information besides just the error message for this to be addressed, and will be ready and willing to do so. Thanks very much!

Karl Lerud

sik · August 14, 2018, 8:21am

Thanks for sharing.

Can you please provide some data, and instructions to see if I can replicate the crash.

sik · August 14, 2018, 8:34am

mean while can you try this for me:

check if openmeeg_hminv.mat, openmeeg_dsm.mat, openmeeg_h2em.mat, opemeeg_gain_eeg.mat flies in /home/pythagoras/.brainstorm/tmp/ they still exist.
cd /home/pythagoras/.brainstorm/openmeeg/linux64 and execute the following line:

LD_LIBRARY_PATH=$PWD ./om_gain --help

if everything worked, and the files exist run:

LD_LIBRARY_PATH=$PWD ./om_gain  -EEG /home/pythagoras/.brainstorm/tmp/openmeeg_hminv.mat /home/pythagoras/.brainstorm/tmp/openmeeg_dsm.mat /home/pythagoras/.brainstorm/tmp/openmeeg_h2em.mat /home/pythagoras/.brainstorm/tmp/openmeeg_gain_eeg.mat

lerud · August 14, 2018, 8:47pm

All those files exist except for openmeeg_gain_eeg.mat, but I tried it anyway. Another segmentation fault:

pythagoras@pythagoras:~/.brainstorm/openmeeg/linux64$ LD_LIBRARY_PATH=$PWD ./om_gain  -EEG /home/pythagoras/.brainstorm/tmp/openmeeg_hminv.mat /home/pythagoras/.brainstorm/tmp/openmeeg_dsm.mat /home/pythagoras/.brainstorm/tmp/openmeeg_h2em.mat /home/pythagoras/.brainstorm/tmp/openmeeg_gain_eeg.mat
./om_gain version 2.4.0 compiled at Jul 13 2018 15:57:20 using OpenMP
 Executing using 12 threads.


| ------ ./om_gain
| -EEG
| /home/pythagoras/.brainstorm/tmp/openmeeg_hminv.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_dsm.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_h2em.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_gain_eeg.mat
| -----------------------

Using variable with name : matrix
Segmentation fault (core dumped)
pythagoras@pythagoras:~/.brainstorm/openmeeg/linux64$

I’d be glad to share whatever data is needed to replicate the error, but I’m not super familiar with FreeSurfer and Brainstorm yet. What would be the minimum things needed to replicate this particular part of the process? My guess is the mat files that Brainstorm has for this protocol so far in its database, for this particular subject. Here are those files, organized into anat and data directories like Brainstorm does. I am attempting to make a head model out of the “mixed” cortex+subcortical. Let me know if this is sufficient, thanks.

https://www.dropbox.com/s/2kjki8hqeojigt8/test.zip?dl=1

Karl

sik · August 15, 2018, 2:03pm

I’m not familiar with brainstorm either, if you can provide me with the openmeeg_xxxxx.mat files that would be great.

meanwhile two things:

in your side ( I don’t think it would have any effect but just in case) change the number of threads from 12 to 1. like this:

LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain  -EEG /home/pythagoras/.brainstorm/tmp/openmeeg_hminv.mat /home/pythagoras/.brainstorm/tmp/openmeeg_dsm.mat /home/pythagoras/.brainstorm/tmp/openmeeg_h2em.mat /home/pythagoras/.brainstorm/tmp/openmeeg_gain_eeg.mat

On my side I’ll try to generate those intermediate files

sik · August 15, 2018, 2:19pm

@francoise could you point me to some tutorial doing something similar to what @lerud is trying to do ? thx.

sik · August 15, 2018, 2:21pm

sorry, I put an extra ‘e’ at the name. @francois can you provide such link?

Francois · August 15, 2018, 2:43pm

The EEG/Epilepsy tutorial you’ve already used?
https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy

Wouldn’t it be better to restore the 2.2 version as the default in Brainstorm while you guys fix all these issues with the new release?..

sik · August 15, 2018, 4:27pm

@francois, I don’t think that reverting to 2.2 is the solution. So far we have mainly encountered openmeeg-brainstorm integration issues (missing libraries, paths, lib incompatibility, etc…) This is the first one with something internal to openmeeg.

What it would be great is to find a manner to replicate brainstorm pipelines so that I can just run script like the epilepsy tutorial and generate the data. I’m sure there’s a way to do so. Its just that I’m not familiar with it.

@lerud could you please try this for me:

set a break point in line 249 of brainstorm3/toolbox/script/tutorial_epilepsy.m
follow the data download steps here https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy#Download_and_installation
open brainstorm
execute tutorial_epilepsy('/path_to/where_you_download_the_zip', '/tmp/report_dir/')

Once the execution has stop at the break point:

cd ~/.brainstorm/openmeeg/linux64
execute LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain -EEG ~/.brainstorm/tmp/openmeeg_hminv.mat ~/.brainstorm/tmp/openmeeg_dsm.mat ~/.brainstorm/tmp/openmeeg_h2em.mat ~/.brainstorm/tmp/openmeeg_gain_eeg.mat

and see if it still segfaults

Francois · August 15, 2018, 5:34pm

You mean: something else that the script tutorial_epilepsy.m ?

sik · August 15, 2018, 6:16pm

That one is completely fine. Something like that one but that breaks

lerud · August 15, 2018, 6:44pm

Here is a zip of everything in my tmp directory after the segmentation fault on my data. And as I mentioned, openmeeg_gain_eeg.mat does not appear in my case:

https://www.dropbox.com/s/pc7iwx8mt062ajk/tmp.zip?dl=1

I tried it with a single thread and the same thing happened.

I did what you suggested with the epilepsy tutorial and it looks like the same commands finish to completion in this case:

pythagoras@pythagoras:~/.brainstorm/openmeeg/linux64$ LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain -EEG ~/.brainstorm/tmp/openmeeg_hminv.mat ~/.brainstorm/tmp/openmeeg_dsm.mat ~/.brainstorm/tmp/openmeeg_h2em.mat ~/.brainstorm/tmp/openmeeg_gain_eeg.mat
./om_gain version 2.4.0 compiled at Jul 13 2018 15:57:20 using OpenMP
 Executing using 1 threads.


| ------ ./om_gain
| -EEG
| /home/pythagoras/.brainstorm/tmp/openmeeg_hminv.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_dsm.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_h2em.mat
| /home/pythagoras/.brainstorm/tmp/openmeeg_gain_eeg.mat
| -----------------------
Using variable with name : matrix
-------------------------------------------
| Elapsed Time: 2.00185 s.
-------------------------------------------
pythagoras@pythagoras:~/.brainstorm/openmeeg/linux64$

Francois · August 15, 2018, 7:04pm

I’m not sure what you expect, and from who. Writing a script that reproduces the crash means that we already know how to reproduce it, hence how to fix it…

sik · August 15, 2018, 8:19pm

Thx, @lerud. I can reproduce.

./om_gain -EEG /tmp/yy/openmeeg_hminv.mat /tmp/yy/openmeeg_dsm.mat /tmp/yy/openmeeg_h2em.mat /tmp/yy/gain_eeg.mat

./om_gain version 2.4.0 compiled at Jun 22 2018 18:01:35 using OpenMP
 Executing using 4 threads.


| ------ ./om_gain
| -EEG
| /tmp/yy/openmeeg_hminv.mat
| /tmp/yy/openmeeg_dsm.mat
| /tmp/yy/openmeeg_h2em.mat
| /tmp/yy/gain_eeg.mat
| -----------------------
Using variable with name : matrix
zsh: segmentation fault (core dumped)  ./om_gain -EEG /tmp/yy/openmeeg_hminv.mat /tmp/yy/openmeeg_dsm.mat

I'll try to do some forensics on it.
here is the ticket:

github.com/openmeeg/openmeeg

[bug] segfault when initializing linop

opened 10:29AM - 16 Aug 18 UTC

closed 05:24PM - 17 Aug 18 UTC

massich

here's the execution with [this data](https://www.dropbox.com/sh/av40f6brhv5qdxn…/AAApYZbe8eC-3-YCV74AvUXNa?dl=0) ```sh ./om_gain -EEG \ ~/Dropbox/openmeeg_segfault/openmeeg_hminv.mat \ ~/Dropbox/openmeeg_segfault/openmeeg_dsm.mat \ ~/Dropbox/openmeeg_segfault/openmeeg_h2em.mat \ /tmp/gain_eeg.mat ./om_gain version 2.4.0 compiled at Aug 15 2018 22:53:28 using OpenMP Executing using 4 threads. | ------ ./om_gain | -EEG | /home/sik/Dropbox/openmeeg_segfault/openmeeg_hminv.mat | /home/sik/Dropbox/openmeeg_segfault/openmeeg_dsm.mat | /home/sik/Dropbox/openmeeg_segfault/openmeeg_h2em.mat | /tmp/gain_eeg.mat | ----------------------- Using variable with name : matrix zsh: segmentation fault (core dumped) ./om_gain -EEG ~/Dropbox/openmeeg_segfault/openmeeg_hminv.mat ``` it breaks here https://github.com/openmeeg/openmeeg/blob/48fb8272f8d4ac88b09cce0c776c48fc483de27a/OpenMEEGMaths/include/linop.h#L148 and this is the trace: ```sh ~/Workspace/openmeeg/build_linux_db/simulate_install_dir/bin master* 16s ❯ lldb -- ./om_gain -EEG \ ~/Dropbox/openmeeg_segfault/openmeeg_hminv.mat \ ~/Dropbox/openmeeg_segfault/openmeeg_dsm.mat \ ~/Dropbox/openmeeg_segfault/openmeeg_h2em.mat \ /tmp/gain_eeg.mat (lldb) target create "./om_gain" Current executable set to './om_gain' (x86_64). (lldb) settings set -- target.run-args "-EEG" "/home/sik/Dropbox/openmeeg_segfault/openmeeg_hminv.mat" "/home/sik/Dropbox/openmeeg_segfault/openmeeg_dsm.mat" "/home/sik/Dropbox/openmeeg_segfault/openmeeg_h2em.mat" "/tmp/gain_eeg.mat" (lldb) r Process 16467 launched: './om_gain' (x86_64) ./om_gain version 2.4.0 compiled at Aug 15 2018 22:53:28 using OpenMP Executing using 1 threads. | ------ ./om_gain | -EEG | /home/sik/Dropbox/openmeeg_segfault/openmeeg_hminv.mat | /home/sik/Dropbox/openmeeg_segfault/openmeeg_dsm.mat | /home/sik/Dropbox/openmeeg_segfault/openmeeg_h2em.mat | /tmp/gain_eeg.mat | ----------------------- Using variable with name : matrix Process 16467 stopped * thread #1, name = 'om_gain', stop reason = signal SIGSEGV: invalid address (fault address: 0x0) frame #0: 0x00007ffff18f0c40 libc.so.6`__memmove_avx_unaligned_erms at memmove-vec-unaligned-erms.S:371 (lldb) bt * thread #1, name = 'om_gain', stop reason = signal SIGSEGV: invalid address (fault address: 0x0) * frame #0: 0x00007ffff18f0c40 libc.so.6`__memmove_avx_unaligned_erms at memmove-vec-unaligned-erms.S:371 frame #1: 0x000055555556998f om_gain`double* std::__copy_move<false, true, std::random_access_iterator_tag>::__copy_m<double>(__first=0x00007fff78f34010, __last=0x0000800099785590, __result=0x00007ffe586e2010) at stl_algobase.h:368 frame #2: 0x0000555555569026 om_gain`double* std::__copy_move_a<false, double const*, double*>(__first=0x00007fff78f34010, __last=0x0000800099785590, __result=0x00007ffe586e2010) at stl_algobase.h:386 frame #3: 0x00005555555683df om_gain`double* std::__copy_move_a2<false, double const*, double*>(__first=0x00007fff78f34010, __last=0x0000800099785590, __result=0x00007ffe586e2010) at stl_algobase.h:424 frame #4: 0x0000555555567c9f om_gain`double* std::copy<double const*, double*>(__first=0x00007fff78f34010, __last=0x0000800099785590, __result=0x00007ffe586e2010) at stl_algobase.h:456 frame #5: 0x000055555556424e om_gain`OpenMEEG::LinOpValue::init(this=0x00005555557cd550, n=605070000, initval=0x00007fff78f34010) at linop.h:148 frame #6: 0x00005555555641ba om_gain`OpenMEEG::LinOpValue::LinOpValue(this=0x00005555557cd550, n=605070000, initval=0x00007fff78f34010) at linop.h:143 frame #7: 0x00007ffff7570307 libOpenMEEGMaths.so.1`OpenMEEG::Matrix::reference_data(this=0x00007fffffffced0, vals=0x00007fff78f34010) at matrix.h:83 frame #8: 0x00007ffff757277f libOpenMEEGMaths.so.1`void OpenMEEG::maths::MatlabIO::read<OpenMEEG::Matrix>(this=0x00007ffff77853a0, mat=0x00005555557c06a0, linop=0x00007fffffffced0) const at MatlabIO.H:287 frame #9: 0x00007ffff7570d66 libOpenMEEGMaths.so.1`OpenMEEG::maths::MatlabIO::read(this=0x00007ffff77853a0, is=0x00007fffffffc9b0, linop=0x00007fffffffced0) const at MatlabIO.H:201 frame #10: 0x00007ffff756d8eb libOpenMEEGMaths.so.1`OpenMEEG::maths::operator>>(mio=0x00007fffffffcc30, linop=0x00007fffffffced0) at MathsIO.C:63 frame #11: 0x00007ffff756703c libOpenMEEGMaths.so.1`OpenMEEG::Matrix::load(this=0x00007fffffffced0, filename="/home/sik/Dropbox/openmeeg_segfault/openmeeg_dsm.mat") at matrix.cpp:264 frame #12: 0x0000555555564842 om_gain`OpenMEEG::Matrix::Matrix(this=0x00007fffffffced0, fname="/home/sik/Dropbox/openmeeg_segfault/openmeeg_dsm.mat") at matrix.h:73 frame #13: 0x0000555555561ee0 om_gain`main(argc=6, argv=0x00007fffffffd148) at gain.cpp:86 frame #14: 0x00007ffff1783b97 libc.so.6`__libc_start_main(main=(om_gain`main at gain.cpp:50), argc=6, argv=0x00007fffffffd148, init=<unavailable>, fini=<unavailable>, rtld_fini=<unavailable>, stack_end=0x00007fffffffd138) at libc-start.c:310 frame #15: 0x000055555556180a om_gain`_start + 42 (lldb) ```

lerud · August 16, 2018, 10:46pm

I see that changes to both OpenMEEG and Matio have been merged. I now get the new error message from OpenMEEG. But how can I utilize the fix that was merged in Matio? Would I have to build and install Matio manually, or will OpenMEEG incorporate the fix somehow?

Karl

sik · August 17, 2018, 4:31pm

Sorry for the delay. As you can se here https://github.com/openmeeg/openmeeg/issues/334#issuecomment-413913953 we have working binaries.

If you want to speed up and baypass the system I think that you can download the OpenMEEG universal linux binaries from https://github.com/openmeeg/openmeeg_packages untar them and swap the old backed for the new one. Like so:

just to make sure that its broken

~/.brainstorm/openmeeg/linux64
❯ LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain -EEG ~/.brainstorm/tmp/openmeeg_hminv.mat ~/.brainstorm/tmp/openmeeg_dsm.mat ~/.brainstorm/tmp/openmeeg_h2em.mat ~/.brainstorm/tmp/openmeeg_gain_eeg.mat
./om_gain version 2.4.0 compiled at Jul 13 2018 15:57:20 using OpenMP
 Executing using 1 threads.


| ------ ./om_gain
| -EEG
| /home/sik/.brainstorm/tmp/openmeeg_hminv.mat
| /home/sik/.brainstorm/tmp/openmeeg_dsm.mat
| /home/sik/.brainstorm/tmp/openmeeg_h2em.mat
| /home/sik/.brainstorm/tmp/openmeeg_gain_eeg.mat
| -----------------------
Using variable with name : matrix
zsh: segmentation fault (core dumped)  LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain -EEG

Keep a copy of the current OpenMEEG backend. (see that there would be 4 broken links)

~/.brainstorm/openmeeg/linux64
❯ mv libOpenMEEG.so.1.1.0 _libOpenMEEG.so.1.1.0

~/.brainstorm/openmeeg/linux64
❯ mv libOpenMEEGMaths.so.1.1.0 _libOpenMEEGMaths.so.1.1.0

~/.brainstorm/openmeeg/linux64
❯ ls -l    
total 152640
lrwxrwxrwx 1 sik sik       21 Jul 13 17:58 libOpenMEEGMaths.so -> libOpenMEEGMaths.so.1
lrwxrwxrwx 1 sik sik       25 Jul 13 17:58 libOpenMEEGMaths.so.1 -> libOpenMEEGMaths.so.1.1.0
-rw-r--r-- 1 sik sik 20966161 Jul 13 17:56 _libOpenMEEGMaths.so.1.1.0
lrwxrwxrwx 1 sik sik       16 Jul 13 17:58 libOpenMEEG.so -> libOpenMEEG.so.1
lrwxrwxrwx 1 sik sik       20 Jul 13 17:58 libOpenMEEG.so.1 -> libOpenMEEG.so.1.1.0
-rw-r--r-- 1 sik sik  1925873 Jul 13 17:57 _libOpenMEEG.so.1.1.0
-rwxr-xr-x 1 sik sik    91362 Jul 13 17:57 om_assemble
-rwxr-xr-x 1 sik sik 14744873 Jul 13 17:57 om_check_geom
-rwxr-xr-x 1 sik sik    37065 Jul 13 17:57 om_forward
-rwxr-xr-x 1 sik sik    83188 Jul 13 17:57 om_gain
-rwxr-xr-x 1 sik sik 14744875 Jul 13 17:57 om_geometry_info
-rwxr-xr-x 1 sik sik 14767946 Jul 13 17:57 om_make_nerve
-rwxr-xr-x 1 sik sik    47597 Jul 13 17:57 om_matrix_convert
-rwxr-xr-x 1 sik sik    31855 Jul 13 17:57 om_matrix_info
-rwxr-xr-x 1 sik sik 14744839 Jul 13 17:57 om_mesh_concat
-rwxr-xr-x 1 sik sik 14768785 Jul 13 17:57 om_mesh_convert
-rwxr-xr-x 1 sik sik 14744813 Jul 13 17:57 om_mesh_info
-rwxr-xr-x 1 sik sik 14745097 Jul 13 17:57 om_mesh_smooth
-rwxr-xr-x 1 sik sik    36507 Jul 13 17:57 om_mesh_to_dip
-rwxr-xr-x 1 sik sik    31471 Jul 13 17:57 om_minverser
-rwxr-xr-x 1 sik sik 14756335 Jul 13 17:57 om_project_sensors
-rwxr-xr-x 1 sik sik 14786966 Jul 13 17:57 om_register_squids
-rwxr-xr-x 1 sik sik    31529 Jul 13 17:57 om_squids2vtk
-rw-r--r-- 1 sik sik       68 Jul 25 17:57 url

Overwrite with the new backend. (see that now the links are proper again)

~/.brainstorm/openmeeg/linux64
❯ cp $PATH_TO_UNZIP/OpenMEEG-2.4.0-Linux/lib/libOpenMEEG.so.1.1.0 ./

~/.brainstorm/openmeeg/linux64
❯ cp $PATH_TO_UNZIP/OpenMEEG-2.4.0-Linux/lib/libOpenMEEGMaths.so.1.1.0 ./ 

~/.brainstorm/openmeeg/linux64 19s
❯ ls -l
total 175168
lrwxrwxrwx 1 sik sik       21 Jul 13 17:58 libOpenMEEGMaths.so -> libOpenMEEGMaths.so.1
lrwxrwxrwx 1 sik sik       25 Jul 13 17:58 libOpenMEEGMaths.so.1 -> libOpenMEEGMaths.so.1.1.0
-rw-r--r-- 1 sik sik 20966161 Jul 13 17:56 _libOpenMEEGMaths.so.1.1.0
-rw-r--r-- 1 sik sik 21121792 Aug 17 18:20 libOpenMEEGMaths.so.1.1.0
lrwxrwxrwx 1 sik sik       16 Jul 13 17:58 libOpenMEEG.so -> libOpenMEEG.so.1
lrwxrwxrwx 1 sik sik       20 Jul 13 17:58 libOpenMEEG.so.1 -> libOpenMEEG.so.1.1.0
-rw-r--r-- 1 sik sik  1925873 Jul 13 17:57 _libOpenMEEG.so.1.1.0
-rw-r--r-- 1 sik sik  1925344 Aug 17 18:20 libOpenMEEG.so.1.1.0
-rwxr-xr-x 1 sik sik    91362 Jul 13 17:57 om_assemble
-rwxr-xr-x 1 sik sik 14744873 Jul 13 17:57 om_check_geom
-rwxr-xr-x 1 sik sik    37065 Jul 13 17:57 om_forward
-rwxr-xr-x 1 sik sik    83188 Jul 13 17:57 om_gain
-rwxr-xr-x 1 sik sik 14744875 Jul 13 17:57 om_geometry_info
-rwxr-xr-x 1 sik sik 14767946 Jul 13 17:57 om_make_nerve
-rwxr-xr-x 1 sik sik    47597 Jul 13 17:57 om_matrix_convert
-rwxr-xr-x 1 sik sik    31855 Jul 13 17:57 om_matrix_info
-rwxr-xr-x 1 sik sik 14744839 Jul 13 17:57 om_mesh_concat
-rwxr-xr-x 1 sik sik 14768785 Jul 13 17:57 om_mesh_convert
-rwxr-xr-x 1 sik sik 14744813 Jul 13 17:57 om_mesh_info
-rwxr-xr-x 1 sik sik 14745097 Jul 13 17:57 om_mesh_smooth
-rwxr-xr-x 1 sik sik    36507 Jul 13 17:57 om_mesh_to_dip
-rwxr-xr-x 1 sik sik    31471 Jul 13 17:57 om_minverser
-rwxr-xr-x 1 sik sik 14756335 Jul 13 17:57 om_project_sensors
-rwxr-xr-x 1 sik sik 14786966 Jul 13 17:57 om_register_squids
-rwxr-xr-x 1 sik sik    31529 Jul 13 17:57 om_squids2vtk
-rw-r--r-- 1 sik sik       68 Jul 25 17:57 url

Try it out (now you should be able to finally see this .brainstorm/tmp/openmeeg_gain_eeg.mat file, that was missing all the time)

~/.brainstorm/openmeeg/linux64
❯ LD_LIBRARY_PATH=$PWD OMP_NUM_THREADS=1 ./om_gain -EEG ~/.brainstorm/tmp/openmeeg_hminv.mat ~/.brainstorm/tmp/openmeeg_dsm.mat ~/.brainstorm/tmp/openmeeg_h2em.mat ~/.brainstorm/tmp/openmeeg_gain_eeg.mat
./om_gain version 2.4.0 compiled at Jul 13 2018 15:57:20 using OpenMP
 Executing using 1 threads.


| ------ ./om_gain
| -EEG
| /home/sik/.brainstorm/tmp/openmeeg_hminv.mat
| /home/sik/.brainstorm/tmp/openmeeg_dsm.mat
| /home/sik/.brainstorm/tmp/openmeeg_h2em.mat
| /home/sik/.brainstorm/tmp/openmeeg_gain_eeg.mat
| -----------------------
Using variable with name: matrix
-------------------------------------------
| Elapsed Time: 18.7218 s.
-------------------------------------------

lerud · August 17, 2018, 5:09pm

Ok, I will try this. But meanwhile, there is apparently another bug in OpenMEEG which is causing my head models being calculated in macOS to be incorrect, even though they were finishing. We are talking about it here:

I have been asked to report this. Would this be easy for you to report and/or diagnose, or should I go to the Github page and make an issue?

Thanks,
Karl

sik · August 17, 2018, 5:40pm

Sure. Be my gest, the more issues we get (and fix) the more reliable the software would be.

you can also find us here https://gitter.im/openmeeg/openmeeg

Alexandre · August 24, 2018, 12:28pm

just to close this thread.

@lerud you should now be able to update brainstorm and get an updated version (2.4.1) of OpenMEEG that should work out of the box.

Alex

lerud · August 24, 2018, 5:04pm

Thank you. OpenMEEG is now producing a gain matrix with no zeros on both Linux and macOS.