[Mne_analysis] Mne_analysis Digest, Vol 80, Issue 6
Kambiz Tavabi
ktavabi at uw.edu
Thu Sep 4 15:59:29 EDT 2014
Hi all,
I tried playing around with the freesurfer VM shortly yesterday. I sudo
installed the MNE nightly build in /usr/local on the VM and sourced
$MNE_ROOT/bin/mne_setup_sh. Next, I ran mne_watershed_bem --subject bert
and got what looked like a missing shared or 32bit library file. I was not
able to figure out exactly what library file because the terminal spat out
gibberish, as if there is also a problem with text encoding. See image
here:
https://www.dropbox.com/s/2pbs9ueu6wtxghz/Screenshot.png?dl=0
I tried installing synaptic package manager and then the
ia32-libs-multiarch libraries package, however the error still persists. If
not an exact reproduction it looks to be a missing ELF interpreter error
affecting the mne_convert_surface & mne_surf2bem programs.
HTH
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 Thu, Sep 4, 2014 at 9:00 AM, <mne_analysis-request at nmr.mgh.harvard.edu>
wrote:
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> Today's Topics:
>
> 1. Re: invalid encoding mne_setup_source_space (Alexandre Gramfort)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Thu, 4 Sep 2014 12:29:32 +0200
> From: Alexandre Gramfort <alexandre.gramfort at telecom-paristech.fr>
> Subject: Re: [Mne_analysis] invalid encoding mne_setup_source_space
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <
> CADeotZqcEM9rbkfO+eenWAL5rwLruqUZ5tN0bQ+KUUh_jYd9kA at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
>
> hi,
>
> in the mean time you can use :
>
> http://neuro.debian.net/vm.html
>
> the neurodebian VM. We use it for teaching. Maybe someone on the list
> can even share with you one that is preconfigured.
>
> no news so far from the freesurfer crowd.
>
> Alex
>
>
> On Thu, Sep 4, 2014 at 11:57 AM, Konstantina Kalogianni
> <K.Kalogianni at tudelft.nl> wrote:
> > 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:
> >>>>
> >>>> Send Mne_analysis mailing list submissions to
> >>>> mne_analysis at nmr.mgh.harvard.edu
> >>>>
> >>>> To subscribe or unsubscribe via the World Wide Web, visit
> >>>>
> >>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>> or, via email, send a message with subject or body 'help' to
> >>>> mne_analysis-request at nmr.mgh.harvard.edu
> >>>>
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> >>>> When replying, please edit your Subject line so it is more specific
> >>>> than "Re: Contents of Mne_analysis digest..."
> >>>>
> >>>>
> >>>> 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>
> >>>>
> >>>> -------------- next part -------------- An HTML attachment was
> >>>> scrubbed...
> >>>> URL:
> >>>> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/2
> >>>> 0
> >>>> 1
> >>>> 40806/b9778457/attachment-0001.html
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> 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
> >>>>>
> >>>>>
> >>>>>
> >>>>> _______________________________________________
> >>>>> Mne_analysis mailing list
> >>>>> Mne_analysis at nmr.mgh.harvard.edu
> >>>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>>>
> >>>>>
> >>>>> The information in this e-mail is intended only for the person to
> >>>>> whom it is addressed. If you believe this e-mail was sent to you in
> >>>>> error and the e-mail contains patient information, please contact
> >>>>> the Partners Compliance HelpLine at
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> >>>> ********************************************
> >>>>
> >>>>
> >>>>
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