[Mne_analysis] invalid encoding mne_setup_source_space
Konstantina Kalogianni
K.Kalogianni at tudelft.nl
Fri Aug 29 10:57:26 EDT 2014
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<mailto: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
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Kambiz Tavabi PhD
Institute for Learning & Brain Sciences
1715 Columbia Road N
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Box 357988
University of Washington
Seattle, WA 98195-7988
Tel: 206-685-6173
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Today's Topics:
1. invalid encoding mne_setup_source_space (Konstantina Kalogianni)
2. Re: Crossing Segmentations (dgw)
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Message: 1
Date: Wed, 6 Aug 2014 21:48:36 +0000
From: Konstantina Kalogianni <K.Kalogianni at tudelft.nl<mailto:K.Kalogianni at tudelft.nl>>
Subject: [Mne_analysis] invalid encoding mne_setup_source_space
To: "mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>"
<mne_analysis at nmr.mgh.harvard.edu<mailto:mne_analysis at nmr.mgh.harvard.edu>>
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<4DF682D3A10EAC46B462A46E16F0B04924B92F0F at SRV364.tudelft.net<mailto:4DF682D3A10EAC46B462A46E16F0B04924B92F0F at SRV364.tudelft.net>>
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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><mailto: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<mailto: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<mailto:mne_analysis at nmr.mgh.harvard.edu>>
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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<mailto: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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