invalid encoding mne_setup_source_space

✉️ Mailing List Archive (read-only)
1

Hi to all,

Thank you for your prompt responses and I am sorry for my delayed one; I was away for a while.
Below I address the points made in your responses:

1. I do have read and write permissions on /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/subjects/

2. In /freesurfer/mne I have read write permissions on all files.

3. I have tried to install MNE in usr/local and I do have all permissions on the folder I have created.
               I do have the same errors though when I repeat the procedure I describe at my first email.
               Is there a recommended location to install mne?

4. In my folder mne/bin some of the files are shell scripts and some of them binary executables.
              Shouldn?t all the files be executables?

5. I only copied the .tar.gz file from windows to linux and nothing more than that.

6. $MNE_ROOT/bin/mne_make_source_space ?help returns: cannot execute binary file.

I guess the problem comes from point 4.
               Do you think is a good idea to install freesurfer and MNE on a linux machine (right now I have it on a virtual machine)?

Thank you.

Best Regards,
Nadia

2

hi Nadia,

can you try a fresh install in your home dir without typing any "sudo".

something like

tar xvzf MNE-Nightly-Linux-x86_64.tar.gz
cd MNE-Nightly-Linux-x86_64
export MNE_ROOT=$PWD
. $MNE_ROOT/bin/mne_setup_sh

Don't forget the ". " before $MNE...

Then export SUBJECTS_DIR with the appropriate path and try again.

Let me know how it goes.

Alex

PS : any volunteer to tackle this issue:

https://github.com/mne-tools/mne-python/issues/960

?

3

Hi Alex,

I did install again mne as you described.
Now when I run mne_watershed_bem I have the COR files and the surf files as before but not the .fif file.
I have a different error though, relating to mne_convert_surface (which is a an executable):
/home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: 2: /home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: : not found
/home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: 1: /home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: /home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: 2: /home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: Syntax error: word unexpected (expecting ")")
/home/fsuser/mne/MNE-2.7.4-3443-Linux-x86_64/bin/mne_convert_surface: ELF : not found

Nadia

4

Nadia,

What is your virtual machine? Can you describe some of the details of it?

Thanks,
D

5

Hi,

Here are the details of the operating system I am running in virtual box:
Operating system: Red Hat (64 bit)
Base memory: 4096 MB
Storage Controller SATA
I have followed the procedure for installing freesurfer in Virtual box described here: https://surfer.nmr.mgh.harvard.edu/fswiki/Installation/FreeSurferVirtualImage.

Thanks,
Nadia

6

hi Nadia,

thanks for letting us know. We need time to reproduce the pb with the virtual
machine and see with FreeSurfer people if we can discuss to have MNE
shipped with the VM. This would be the best long term way to go.

Anybody has this VM to see if he can reproduce?

We'll keep you posted.

Alex

7

Hi Alex,
Thank you for your reply.
It will be a nice feature if at some point MNE is inside the VM along with freesurfer.
Meanwhile do you suggest to install MNE on the latest Red Hat Linux distribution?
Nadia

8

hi,

in the mean time you can use :

http://neuro.debian.net/vm.html

the neurodebian VM. We use it for teaching. Maybe someone on the list
can even share with you one that is preconfigured.

no news so far from the freesurfer crowd.

Alex

9

Hi Nadia,

It turns out that the FreeSurfer VM needs a 32bits version of MNE.

so install the nightly i686 (not the x86_64) version of MNE and copy
to the lib folder the libgfortran.so.1 that you can find at

https://dl.dropboxusercontent.com/u/2140486/libgfortran.so.1.i686.zip

I am on my way to make a new VM with FreeSurfer + MNE + MNE-Python so
it will become more straightforward.

Let me know if you have any trouble.

Best,
Alex

10

forward to the list.

11

This is great! Thanks. The FreeSurfer VM is indeed 32 bits, but the
next version I am working on (if I finish it) will be 64 bits. The
images on the FS wiki have been updated to indicate that the current
version is actually 32 bits.

D