[Mne_analysis] Mne_analysis Digest, Vol 79, Issue 12

Thu Aug 7 17:05:00 EDT 2014

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
> 
> You can reach the person managing the list at
>         mne_analysis-owner at nmr.mgh.harvard.edu
> 
> 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/20140806/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
> > http://www.partners.org/complianceline . If the e-mail was sent to you in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
> >
> -------------- next part --------------
> An HTML attachment was scrubbed...
> URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140806/86581b22/attachment.html
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Screen Shot 2014-08-06 at 1.13.20 PM.png
> Type: image/png
> Size: 62870 bytes
> Desc: not available
> Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140806/86581b22/attachment.png
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Screen Shot 2014-08-06 at 1.28.46 PM.png
> Type: image/png
> Size: 124960 bytes
> Desc: not available
> Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140806/86581b22/attachment-0001.png
> -------------- next part --------------
> A non-text attachment was scrubbed...
> Name: Screen Shot 2014-08-06 at 1.25.14 PM.png
> Type: image/png
> Size: 154778 bytes
> Desc: not available
> Url : http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140806/86581b22/attachment-0002.png
> 
> ------------------------------
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 
> End of Mne_analysis Digest, Vol 79, Issue 12
> ********************************************
> 
> _______________________________________________
> Mne_analysis mailing list
> Mne_analysis at nmr.mgh.harvard.edu
> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis

-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20140807/6a63f87e/attachment.html 