[Mne_analysis] invalid encoding mne_setup_source_space

Konstantina Kalogianni K.Kalogianni at tudelft.nl
Thu Sep 4 05:57:28 EDT 2014
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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

-----Original Message-----
From: mne_analysis-bounces at nmr.mgh.harvard.edu [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Alexandre Gramfort
Sent: woensdag 3 september 2014 21:59
To: Discussion and support forum for the users of MNE Software
Subject: Re: [Mne_analysis] invalid encoding mne_setup_source_space

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


On Tue, Sep 2, 2014 at 6:44 PM, Konstantina Kalogianni <K.Kalogianni at tudelft.nl> wrote:
> 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
>
>
>
> -----Original Message-----
> From: mne_analysis-bounces at nmr.mgh.harvard.edu 
> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of dgw
> Sent: dinsdag 2 september 2014 17:02
> To: Discussion and support forum for the users of MNE Software
> Subject: Re: [Mne_analysis] invalid encoding mne_setup_source_space
>
> Nadia,
>
> What is your virtual machine? Can you describe some of the details of it?
>
> Thanks,
> D
>
> On Tue, Sep 2, 2014 at 10:28 AM, Konstantina Kalogianni <K.Kalogianni at tudelft.nl> wrote:
>> 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
>>
>> -----Original Message-----
>> From: mne_analysis-bounces at nmr.mgh.harvard.edu
>> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of 
>> Alexandre Gramfort
>> Sent: vrijdag 29 augustus 2014 19:10
>> To: Discussion and support forum for the users of MNE Software
>> Subject: Re: [Mne_analysis] invalid encoding mne_setup_source_space
>>
>> 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
>>
>> ?
>>
>>
>> On Fri, Aug 29, 2014 at 4:57 PM, Konstantina Kalogianni <K.Kalogianni at tudelft.nl> wrote:
>>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> From: mne_analysis-bounces at nmr.mgh.harvard.edu
>>> [mailto:mne_analysis-bounces at nmr.mgh.harvard.edu] On Behalf Of Matti 
>>> Hamalainen
>>> Sent: donderdag 7 augustus 2014 23:05
>>> To: Discussion and support forum for the users of MNE Software
>>> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 79, Issue 12
>>>
>>>
>>>
>>>
>>>
>>> Again, try what happens when you run
>>>
>>>
>>>
>>> $MNE_ROOT/bin/mne_make_source_space --help
>>>
>>>
>>>
>>> - Matti
>>>
>>>
>>>
>>>
>>>
>>> On Aug 6, 2014, at 9:47 PM, Kambiz Tavabi <ktavabi at uw.edu> wrote:
>>>
>>>
>>>
>>> Nadia,
>>>
>>> Is there a particular reason for why mne appears to be installed 
>>> within your freesurfer directory? Can you confirm you have write 
>>> permission on 
>>> /usr/local/freesurfer/mne/MNE-2.7.0-3106-Linux-x86_64/subjects/
>>>
>>> This is not the recommended directory structure on a linux environment.
>>>
>>>
>>>
>>> regards,
>>>
>>> Kam
>>>
>>>
>>> ------------------------------------------------------------
>>> Kambiz Tavabi PhD
>>> Institute for Learning & Brain Sciences
>>> 1715 Columbia Road N
>>> Portage Bay Building
>>> Box 357988
>>> University of Washington
>>> Seattle, WA 98195-7988
>>> Tel: 206-685-6173
>>> ------------------------------------------------------------
>>>
>>>
>>>
>>> On Wed, Aug 6, 2014 at 2:53 PM,
>>> <mne_analysis-request at nmr.mgh.harvard.edu>
>>> wrote:
>>>
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>>> Today's Topics:
>>>
>>>    1. invalid encoding mne_setup_source_space (Konstantina Kalogianni)
>>>    2. Re: Crossing Segmentations (dgw)
>>>
>>>
>>> --------------------------------------------------------------------
>>> -
>>> -
>>>
>>> Message: 1
>>> Date: Wed, 6 Aug 2014 21:48:36 +0000
>>> From: Konstantina Kalogianni <K.Kalogianni at tudelft.nl>
>>> Subject: [Mne_analysis] invalid encoding mne_setup_source_space
>>> To: "mne_analysis at nmr.mgh.harvard.edu"
>>>         <mne_analysis at nmr.mgh.harvard.edu>
>>> Message-ID:
>>>         
>>> <4DF682D3A10EAC46B462A46E16F0B04924B92F0F at SRV364.tudelft.net>
>>> Content-Type: text/plain; charset="us-ascii"
>>>
>>> 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<mailto:k.kalogianni at tudelft.nl>
>>>
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>>> ------------------------------
>>>
>>> Message: 2
>>> Date: Wed, 6 Aug 2014 17:52:44 -0400
>>> From: dgw <dgwakeman at gmail.com>
>>> Subject: Re: [Mne_analysis] Crossing Segmentations
>>> To: Discussion and support forum for the users of MNE Software
>>>         <mne_analysis at nmr.mgh.harvard.edu>
>>> Message-ID:
>>>
>>> <CADM2BTjgBKS3bLPYZH1RqN6-SpiQO8_MF6H5-hb-jKMOBmFo_A at mail.gmail.com>
>>> Content-Type: text/plain; charset="utf-8"
>>>
>>> Hi Isaiah,
>>>
>>> I can't see the crossing in the images (if you make the surfaces 
>>> visible in the 2d slice you can actually visualize all the places 
>>> the surfaces cross easier; especially, because you can see all three 
>>> at once not just the outermost), but I'll take your word for it. The 
>>> bumps shouldn't be a problem for doing the calculations, but I 
>>> wonder whether you think they exist in reality (how well does the 
>>> surface line up with the skin surface when moving through the 2d slices?).
>>> Unfortunately, the poor lower skull coverage in your MRI will force 
>>> you to either try some hacks to get surfaces, which don't cross. 
>>> (For future studies, you may want to make sure to include all of the 
>>> skull with maybe a little extra cushion space on top of that).
>>>
>>> The only way i can think of to try to make this work is to try to 
>>> paint (using tkmedit, or freeview) on a copy of the T1 extra 
>>> material below to give the surface production something else to latch onto.
>>> You might be able to copy in matlab some data from the sample head 
>>> if you can line up the lower portions somewhat. These are very hacky 
>>> solutions, but they are the only ones which I can think of for this 
>>> problem. Unfortunately, I'm guessing your T1 doesn't have any 
>>> cerebellum coverage, which is likely a large part of the problem. 
>>> You really, need an image which includes all of the skull to fit surfaces around it well.
>>>
>>> HTH,
>>> D
>>>
>>>
>>>
>>> On Wed, Aug 6, 2014 at 5:28 PM, Isaiah C. Smith < 
>>> Isaiah.C.Smith.17 at dartmouth.edu> wrote:
>>>
>>>>
>>>>  Hello All,
>>>>
>>>> Thank you for the help. I looked at my surface images in free view 
>>>> and they are crossing. The crossing seems to be taking place 
>>>> between the the brain and inner skull crossing over outer skull and 
>>>> outer skin. I believe that this is because the data that we have 
>>>> only goes down so far in the original mr images (Below). And when 
>>>> the individual surfaces are created they cross towards the 
>>>> posterior part of the head (Next Image). I attached the surfaces 
>>>> just in case to allow you to see. Would it be possible to extend 
>>>> outer skull and skin when using freesurfer, or get around this some 
>>>> other way. And lastly we are getting a very bumpy skin (Last 
>>>> Photo). Will this be a problem when creating the head model, finding the lead field matrix, etc.
>>>> with MNE with MATLAB because the crossing sections prevent me from proceeding?
>>>>
>>>> Isaiah
>>>>
>>>>
>>>>
>>>> _______________________________________________
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