[Mne_analysis] newbie question

Wed Feb 22 08:55:21 EST 2012

Hi Andy, 

although your method solved your problem - I would not recommend it in general. 
Normally, a standard procedure to install the relevant libraries puts them into directories which are already scanned during program starts or extents the search list accordingly. If this, however, fails because the world is never perfect - there are the manual methods below to get the stuff repaired. 

You can extent the list of pathes where linux searches for the shared libraries via LD_LIBRARYPATH (A) or via configuration files (B): 

(A) 
echo $LD_LIBRARY_PATH # if you see some output here use a), otherwise b) 
a) 
export LD_LIBRARY_PATH= ${LD_LIBRARY_PATH }:<where your libgfortran.so.1 is located> 
b) 
export LD_LIBRARY_PATH= <where your libgfortran.so.1 is located> 

This is going to work in the existing shell until you close it (or logoff). 

(B) 
A more persistent way is this - provided you have superuser rights on your machine: 

You should find a directory /etc/ld.so.conf.d/ at your machine. Additionally, there should be a file /etc/ld.so.conf mentioning this directory as to be included. 
Create a new file within the directory and simply put the directory name in it. 
run ldconfig to update the cache for the shared libraries. 

There are other methods as well ... as always :) 
http://prefetch.net/articles/linkers.badldlibrary.html 

best wishes, 
Burkhard 

-- 
Dr. Burkhard Maess 
Max Planck Institute for Human Cognitive and Brain Sciences 
Stephanstr. 1a, P.O. Box 500355, D-04303 Leipzig 
Aussenstelle Bennewitz, phone/fax: +49(3425)8875-2526/-2511 mail: maess 'at' cbs.mpg.de, http://www.cbs.mpg.de 

----- Original Message -----
From: "Andrew R. Dykstra" <Andrew.Dykstra at med.uni-heidelberg.de> 
To: "mne analysis" <mne_analysis at nmr.mgh.harvard.edu> 
Sent: Wednesday, 22 February, 2012 10:08:33 AM 
Subject: Re: [Mne_analysis] newbie question 

Thanks for the replies everyone. Just to follow up, I downloaded the nightly build (from 21. Feb 2012) of MNE and indeed multiple events can now be included in a category. But, I ran into the following error when attempting to run mne_browse_raw: 

mne_browse_raw: error while loading shared libraries: libgfortran.so.1: cannot open shared object file: No such file or directory 

I already had the library in question from an install of the enthought python distribution, but no link to it where MNE was looking. 

ln -s <where your libgfortran.so.1 is located> /usr/lib/libgfortran.so.1 

solved the problem. 

Andy 

On Tue, Feb 21, 2012 at 7:34 PM, Matti Hamalainen < msh at nmr.mgh.harvard.edu > wrote: 

On Feb 21, 2012, at 11:25 AM, Stephen Politzer-Ahles wrote: 

Matti, 

That's great news, this sounds like it'll be much easier than rewriting event files! Just out of curiosity, does this also work with mne_process_raw in batch mode (with .ave or .cov definition files)? 

Yes, this applies to the ave and cov files. 

- Matti 

Best, 
Steve Politzer-Ahles 

On Tue, Feb 21, 2012 at 10:20 AM, Matti Hamalainen < msh at nmr.mgh.harvard.edu <mailto: msh at nmr.mgh.harvard.edu >> wrote: 

Hi Andrew, 

The mne_browse_raw in the nightly build of MNE now available on the web site you can specify 

event 11 
event 12 
etc. 

within a category to have multiple events averaged together. 

- Matti 

On Feb 21, 2012, at 10:58 AM, Andrew R. Dykstra wrote: 

> Hi all, 
> 
> I'm trying to specify multiple event codes in a category for averaging and can't figure out the syntax for doing so. What I've tried is below. How does one do this? 
> 
> category { 
> name "Category 1" 
> event 11 12 13 21 22 23 31 32 33 
> # event 12 
> # event 13 
> # event 21 
> # event 22 
> # event 23 
> # event 31 
> # event 32 
> # event 33 
> tmin -0.1 
> tmax 0.7 
> color 0.91 0.47 0.09 
> } 
> category { 
> name "Category 2" 
> event 10 20 30 
> # event 20 
> # event 30 
> tmin -0.1 
> tmax 0.7 
> color 0.075 0.61 0.93 
> } 
> 
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-- 
Stephen Politzer-Ahles 
University of Kansas 
Linguistics Department 
http://www.linguistics.ku.edu/ 

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