[Mne_analysis] Mne_analysis Digest, Vol 80, Issue 9
annett schirmer
psysa at nus.edu.sg
Mon Sep 8 12:30:38 EDT 2014
Thanks Hari, that worked.
Cheers,
Annett
On Monday 08,September,2014 04:46 PM,
mne_analysis-request at nmr.mgh.harvard.edu wrote:
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> Today's Topics:
>
> 1. Re: bdf import issue (Hari Bharadwaj)
> 2. Re: bdf import issue (Hari Bharadwaj)
> 3. Re: Mne_analysis Digest, Vol 80, Issue 6 (Konstantina Kalogianni)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sun, 7 Sep 2014 12:17:20 -0400
> From: Hari Bharadwaj <hari at nmr.mgh.harvard.edu>
> Subject: Re: [Mne_analysis] bdf import issue
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <F4C1DDFA-CDC7-4EFC-A3EB-2C2B0C571FA1 at nmr.mgh.harvard.edu>
> Content-Type: text/plain; charset="us-ascii"
>
> Hi Annett,
> The following is a hpts version of the standard 64 channel Biosemi layout (and also includes standard cardinal point locations) which you could download and provide for the hpts argument when importing...
> https://github.com/mne-tools/mne-python/blob/master/mne/io/edf/tests/data/biosemi.hpts
>
> Regarding, not being able to see the channels, I think you just need to add your channel names (probable A1-32 and B1-32) to the channel selection...it seems like the data were imported successfully. You could do that from the channel selection drop down menu of mne_browse_raw and using "Add.." button.
>
> HTH,
> Hari
>
> Hari Bharadwaj
> Martinos Center for Biomedical Imaging,
> Massachusetts General Hospital
> Charlestown, MA 02129
>
> hari at nmr.mgh.harvard.edu
> Ph: 734-883-5954
>
>> On Sep 7, 2014, at 7:05 AM, annett schirmer <psysa at nus.edu.sg> wrote:
>>
>> Hi,
>>
>> I'm trying to import a bdf file using the mne_edf2fiff function and have
>> run into two problems.
>>
>> 1) I don't have a proper elp or hpts file. Can someone please share or
>> let me know how the information provided by Biosemi
>> (http://www.biosemi.com/headcap.htm) can be converted properly?
>>
>> 2) I don't get an error message when I load the converted fif into
>> mne_browse_raw. However, the display window remains empty.
>>
>> Thanks!
>> Annett
>>
>> ######
>>
>> annett at asuspc:~/APPLICATIONS/MNE/MNE_TRIAL$ mne_browse_raw --raw 1.fif
>> --digtrig Status
>> Using a 4096-point FFT in filtering of raw data with 2048-sample tapers
>> bandpass = 0.0 ( 0.0) ... 40.0 ( 5.0) Hz
>> filter is on
>> 64-bit architecture. Using 2000.00 Mbytes for ring buffers
>> 24 selections loaded from
>> /home/annett/APPLICATIONS/MNE/MNE-2.7.0-3106-Linux-x86_64/share/mne/mne_browse_raw/mne_browse_raw.sel
>> Current selection is Vertex
>> Initial settings data created.
>>
>> --- Opening /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif ---
>>
>> No compensation data in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>> Compensation in file : uncompensated
>> Setting up compensation data...
>> No compensation set. Nothing more to do.
>> No compensation was requested.
>> A new compensation value (uncompensated) was assigned to 0 MEG channels.
>> No SSS data in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>> 0 bad channels read from /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>> filter : 0.000 ... 40.0 Hz bins : 0 ... 1280 of 4097 hpw : 3 lpw : 80
>> Highpass filter will work as specified.
>> Initial dc offsets determined
>> Raw data file /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif:
>> nchan = 73
>> nsamp = 325376
>> sfreq = 256.000 Hz
>> length = 1271.000 sec
>> Scanning Status for triggers...[done]
>> 1030 events found in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>> 1030 events written to /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1-eve.fif
>> Trigger channel : Status max_event : 0
>> No projection operator found in
>> /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>> Average EEG reference projection added.
>>
>> --- Projection status ---
>>
>> # 1 : Average EEG reference : 1 vecs : 72 chs EEG active
>>
>> --- Complete ---
>>
>> --
>> Dr. Annett Schirmer
>> Associate Professor
>> Department of Psychology
>> Faculty of Arts and Social Sciences
>> National University of Singapore
>> Block AS4, Level 2
>> 9 Arts Link
>> Singapore 117570
>>
>> Tel: ++65 6516 8703
>> Fax: ++65 6773 1843
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>
>>
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> ------------------------------
>
> Message: 2
> Date: Sun, 07 Sep 2014 12:42:23 -0400
> From: Hari Bharadwaj <hari at nmr.mgh.harvard.edu>
> Subject: Re: [Mne_analysis] bdf import issue
> To: Discussion and support forum for the users of MNE Software
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID: <db5c2c02-0b01-41df-8a06-defcaa5d8f9e at email.android.com>
> Content-Type: text/plain; charset="utf-8"
>
> This is the same file with the Bio semi names rather than the 10-20 names:
> https://github.com/haribharadwaj/ANLffr/blob/master/anlffr/helper/sysfiles/biosemi64.hpts
>
>
>
> Hari Bharadwaj <hari at nmr.mgh.harvard.edu> wrote:
>
>> Hi Annett,
>> The following is a hpts version of the standard 64 channel Biosemi
>> layout (and also includes standard cardinal point locations) which you
>> could download and provide for the hpts argument when importing...
>> https://github.com/mne-tools/mne-python/blob/master/mne/io/edf/tests/data/biosemi.hpts
>>
>> Regarding, not being able to see the channels, I think you just need to
>> add your channel names (probable A1-32 and B1-32) to the channel
>> selection...it seems like the data were imported successfully. You
>> could do that from the channel selection drop down menu of
>> mne_browse_raw and using "Add.." button.
>>
>> HTH,
>> Hari
>>
>> Hari Bharadwaj
>> Martinos Center for Biomedical Imaging,
>> Massachusetts General Hospital
>> Charlestown, MA 02129
>>
>> hari at nmr.mgh.harvard.edu
>> Ph: 734-883-5954
>>
>>> On Sep 7, 2014, at 7:05 AM, annett schirmer <psysa at nus.edu.sg> wrote:
>>>
>>> Hi,
>>>
>>> I'm trying to import a bdf file using the mne_edf2fiff function and
>> have
>>> run into two problems.
>>>
>>> 1) I don't have a proper elp or hpts file. Can someone please share
>> or
>>> let me know how the information provided by Biosemi
>>> (http://www.biosemi.com/headcap.htm) can be converted properly?
>>>
>>> 2) I don't get an error message when I load the converted fif into
>>> mne_browse_raw. However, the display window remains empty.
>>>
>>> Thanks!
>>> Annett
>>>
>>> ######
>>>
>>> annett at asuspc:~/APPLICATIONS/MNE/MNE_TRIAL$ mne_browse_raw --raw
>> 1.fif
>>> --digtrig Status
>>> Using a 4096-point FFT in filtering of raw data with 2048-sample
>> tapers
>>> bandpass = 0.0 ( 0.0) ... 40.0 ( 5.0) Hz
>>> filter is on
>>> 64-bit architecture. Using 2000.00 Mbytes for ring buffers
>>> 24 selections loaded from
>>>
>> /home/annett/APPLICATIONS/MNE/MNE-2.7.0-3106-Linux-x86_64/share/mne/mne_browse_raw/mne_browse_raw.sel
>>> Current selection is Vertex
>>> Initial settings data created.
>>>
>>> --- Opening /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif ---
>>>
>>> No compensation data in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>>> Compensation in file : uncompensated
>>> Setting up compensation data...
>>> No compensation set. Nothing more to do.
>>> No compensation was requested.
>>> A new compensation value (uncompensated) was assigned to 0 MEG
>> channels.
>>> No SSS data in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>>> 0 bad channels read from
>> /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>>> filter : 0.000 ... 40.0 Hz bins : 0 ... 1280 of 4097 hpw : 3
>> lpw : 80
>>> Highpass filter will work as specified.
>>> Initial dc offsets determined
>>> Raw data file /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif:
>>> nchan = 73
>>> nsamp = 325376
>>> sfreq = 256.000 Hz
>>> length = 1271.000 sec
>>> Scanning Status for triggers...[done]
>>> 1030 events found in /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>>> 1030 events written to
>> /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1-eve.fif
>>> Trigger channel : Status max_event : 0
>>> No projection operator found in
>>> /home/annett/APPLICATIONS/MNE/MNE_TRIAL/1.fif
>>> Average EEG reference projection added.
>>>
>>> --- Projection status ---
>>>
>>> # 1 : Average EEG reference : 1 vecs : 72 chs EEG active
>>>
>>> --- Complete ---
>>>
>>> --
>>> Dr. Annett Schirmer
>>> Associate Professor
>>> Department of Psychology
>>> Faculty of Arts and Social Sciences
>>> National University of Singapore
>>> Block AS4, Level 2
>>> 9 Arts Link
>>> Singapore 117570
>>>
>>> Tel: ++65 6516 8703
>>> Fax: ++65 6773 1843
>>>
>>> _______________________________________________
>>> Mne_analysis mailing list
>>> Mne_analysis at nmr.mgh.harvard.edu
>>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
>>>
>>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Mne_analysis mailing list
>> Mne_analysis at nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> --
> Sent from my Android phone with K-9 Mail. Please excuse my brevity.
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> ------------------------------
>
> Message: 3
> Date: Mon, 8 Sep 2014 08:46:25 +0000
> From: Konstantina Kalogianni <K.Kalogianni at tudelft.nl>
> Subject: Re: [Mne_analysis] Mne_analysis Digest, Vol 80, Issue 6
> To: Kambiz Tavabi <ktavabi at uw.edu>,
> "<Mne_analysis at nmr.mgh.harvard.edu>"
> <mne_analysis at nmr.mgh.harvard.edu>
> Message-ID:
> <4DF682D3A10EAC46B462A46E16F0B04924BAF3BE at SRV364.tudelft.net>
> Content-Type: text/plain; charset="utf-8"
>
> Hi all,
> This is exactly what I am getting.
> Regards,
> Nadia
>
> From: Kambiz Tavabi [mailto:ktavabi at uw.edu]
> Sent: donderdag 4 september 2014 21:59
> To: <Mne_analysis at nmr.mgh.harvard.edu>
> Cc: Alexandre Gramfort; Konstantina Kalogianni
> Subject: Re: Mne_analysis Digest, Vol 80, Issue 6
>
> 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<mailto:mne_analysis-request at nmr.mgh.harvard.edu>> wrote:
> Send Mne_analysis mailing list submissions to
> mne_analysis at nmr.mgh.harvard.edu<mailto: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<mailto: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<mailto: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. 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<mailto: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<mailto:mne_analysis at nmr.mgh.harvard.edu>>
> Message-ID:
> <CADeotZqcEM9rbkfO+eenWAL5rwLruqUZ5tN0bQ+KUUh_jYd9kA at mail.gmail.com<mailto:CADeotZqcEM9rbkfO%2BeenWAL5rwLruqUZ5tN0bQ%2BKUUh_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<mailto: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> [mailto: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<mailto: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>
>>> [mailto: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<mailto: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>
>>>> [mailto: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<mailto: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>
>>>>> [mailto: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
>>>>>
>>>>>
>>>>> ------------------------------------------------------------
>>>>> 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<tel:206-685-6173>
>>>>> ------------------------------------------------------------
>>>>>
>>>>>
>>>>>
>>>>> On Wed, Aug 6, 2014 at 2:53 PM,
>>>>> <mne_analysis-request at nmr.mgh.harvard.edu<mailto:mne_analysis-request at nmr.mgh.harvard.edu>>
>>>>> wrote:
>>>>>
>>>>> Send Mne_analysis mailing list submissions to
>>>>> mne_analysis at nmr.mgh.harvard.edu<mailto: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<mailto:mne_analysis-request at nmr.mgh.harvard.edu>
>>>>>
>>>>> You can reach the person managing the list at
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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<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>>
>>>>> Message-ID:
>>>>>
>>>>> <4DF682D3A10EAC46B462A46E16F0B04924B92F0F at SRV364.tudelft.net<mailto: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><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>>
>>>>> Message-ID:
>>>>>
>>>>> <CADM2BTjgBKS3bLPYZH1RqN6-SpiQO8_MF6H5-hb-jKMOBmFo_A at mail.gmail.com<mailto: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<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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