[Mne_analysis] invalid encoding mne_setup_source_space
Konstantina Kalogianni
K.Kalogianni at tudelft.nl
Tue Sep 2 12:44:53 EDT 2014
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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