[Mne_analysis] invalid encoding mne_setup_source_space

[Matti Hamalainen]

It looks like the binary file $MNE_ROOT/bin/mne_make_source_space is being interpreted as a shell script. Do you have the same problem trying to run any other executable from $MNE_ROOT/bin? Sounds like the binaries may have been somehow damaged in transit. 

Have you by any chance copied the MNE stuff to and from a Windows volume?

- Matti

On Aug 7, 2014, at 9:00 AM, Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr> wrote:

> hi,
> 
> let us know if Kam's answer helps or not.
> 
> Best,
> Alex
> 
> On Wed, Aug 6, 2014 at 11:48 PM, Konstantina Kalogianni
> <K.Kalogianni at tudelft.nl> wrote:
>> Dear MNE community,
>> 
>> 
>> 
>> I am new in using MNE and I have a question that relates to invalid
>> encoding.
>> 
>> 
>> 
>> I am having  a  problem with the use of the function mne_setup_source_space.
>> 
>> 
>> 
>> Let me explain how I reached to the error: after running freesurfer
>> (installed on linux on virtual box) on one of my MRI scans I have installed
>> mne  with the following commands:
>> 
>> export MNE_ROOT=<MNE directory>
>> 
>> cd $MNE_ROOT/bin
>> 
>> . ./mne_setup_sh
>> 
>> This was completed without an error.
>> 
>> 
>> 
>> Then I have set my subjects’ directory with:
>> 
>> export SUBJECTS_DIR=<MNE ANALYSIS DIR>/subjects
>> 
>> export SUBJECT=<subject's name>
>> 
>> 
>> 
>> Then I run:  mne_setup_source_space --ico -6 and it produces the following
>> error.:
>> 
>> 
>> 
>>>>> 1. Creating the source space file
>>>>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/subjects/teo/bem/teo-oct-6-src.fif...
>> 
>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/bin/mne_make_source_space:
>> 2:
>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/bin/mne_make_source_space:
>> Syntax error: Unterminated quoted string
>> 
>> Source space creation failed
>> 
>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/bin/mne_make_source_space:
>> 1:
>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/bin/mne_make_source_space:
>> ELF[1][1]: not found
>> 
>> 
>> 
>> Apparently is searching for a file with wrong encoding.
>> 
>> 
>> 
>> Is there something else I should do to make it run?
>> 
>> I have installed already netpbm successfully but I had the same problem when
>> running mne_setup_source_space.
>> 
>> I also have  set the encoding to utf-8 but no change in my error.
>> 
>> 
>> 
>> Another  thing is that  I am able to run mne_watershed_bem and create the
>> .surf files the .COR files but at the end an error appears and I don’t have
>> the .fif files in my bem/watershed folder or bem/watershed/ws folder.
>> 
>> Also an error related to encoding appears so I guess the 2 errors are
>> related.
>> 
>> 
>> 
>> Can you please help in solving this issue?
>> 
>> Thank you.
>> 
>> Best Regards,
>> 
>> 
>> 
>> K. (Nadia) Kalogianni
>> 
>> PhD candidate
>> 
>> 
>> 
>> TU Delft / Department of Biomechanical Engineering
>> Mekelweg 2
>> 2628 CD Delft
>> Room: 34-H-3-320
>> T +31 15-27 84230
>> E  k.kalogianni at tudelft.nl
>> 
>> 
>> 
>> 
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---------

Matti Hamalainen, Ph.D.
Athinoula A. Martinos Center for Biomedical Imaging
Massachusetts General Hospital

msh at nmr.mgh.harvard.edu
mhamalainen at partners.org