[Mne_analysis] invalid encoding mne_setup_source_space
Konstantina Kalogianni
K.Kalogianni at tudelft.nl
Tue Sep 2 10:28:55 EDT 2014
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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