<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:st1="urn:schemas-microsoft-com:office:smarttags" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv=Content-Type content="text/html; charset=iso-8859-1">
<meta name=Generator content="Microsoft Word 11 (filtered medium)">
<!--[if !mso]>
<style>
v\:* {behavior:url(#default#VML);}
o\:* {behavior:url(#default#VML);}
w\:* {behavior:url(#default#VML);}
.shape {behavior:url(#default#VML);}
</style>
<![endif]--><o:SmartTagType
namespaceuri="urn:schemas-microsoft-com:office:smarttags"
name="metricconverter"/>
<!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }
</style>
<![endif]-->
<style>
<!--
/* Font Definitions */
@font-face
{font-family:Helvetica;
panose-1:2 11 6 4 2 2 2 2 2 4;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:12.0pt;
font-family:"Times New Roman";}
a:link, span.MsoHyperlink
{color:blue;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{color:blue;
text-decoration:underline;}
p
{mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman";}
span.EmailStyle18
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:595.3pt 841.9pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.Section1
{page:Section1;}
-->
</style>
</head>
<body lang=FR link=blue vlink=blue>
<div class=Section1>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Dear all,<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>I have a question about
conversion of fif file into mat file;. I would like to convert my raw data (fif
file) into matlab file. For this, I tried to use the function
mne_convert_mne_data but I have a message "no evoked data here". I have
the same message if I try this with averaged data (fif file) directly obtained
by on-line averaging. <o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>I exactly wrote this
command line:<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>mne_convert_mne_data –meas
my filename.fif –mat –out my filename.mat<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Something is wrong ?<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Thanks for your help !<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Bye<o:p></o:p></span></font></p>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'><o:p> </o:p></span></font></p>
<div>
<p class=MsoNormal><font size=2 color=navy face=Arial><span lang=EN-GB
style='font-size:10.0pt;font-family:Arial;color:navy'>Etienne LABYT</span></font><font
color=navy><span lang=EN-GB style='color:navy'><o:p></o:p></span></font></p>
</div>
<div>
<div class=MsoNormal align=center style='text-align:center'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>
<hr size=2 width="100%" align=center tabindex=-1>
</span></font></div>
<p class=MsoNormal><b><font size=2 face=Tahoma><span style='font-size:10.0pt;
font-family:Tahoma;font-weight:bold'>De :</span></font></b><font size=2
face=Tahoma><span style='font-size:10.0pt;font-family:Tahoma'> mne_analysis-bounces@nmr.mgh.harvard.edu
[mailto:mne_analysis-bounces@nmr.mgh.harvard.edu] <b><span style='font-weight:
bold'>De la part de</span></b> Gustavo Sudre<br>
<b><span style='font-weight:bold'>Envoyé :</span></b> mardi 14 avril 2009
18:05<br>
<b><span style='font-weight:bold'>À :</span></b> Matti Hamalainen<br>
<b><span style='font-weight:bold'>Cc :</span></b>
Mne_analysis@nmr.mgh.harvard.edu<br>
<b><span style='font-weight:bold'>Objet :</span></b> Re: [Mne_analysis]
averaging in MNE</span></font><o:p></o:p></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'>Matti,<br>
<br>
That worked great. Thanks!<br>
<br>
Best,<br>
<br>
Gus<br>
<br>
<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Tue, Apr 14, 2009 at 6:44 AM, Matti Hamalainen <<a
href="mailto:msh@nmr.mgh.harvard.edu">msh@nmr.mgh.harvard.edu</a>> wrote:<o:p></o:p></span></font></p>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>HI Gustavo,<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
<div>
<div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>On Apr 13, 2009, at 10:39 AM, Gustavo Sudre wrote:<o:p></o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<blockquote style='margin-top:5.0pt;margin-bottom:5.0pt' type=cite>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Hello,<br>
<br>
I have a couple questions regarding averaging MEG data with MNE and I was
wondering if you could help me.<br>
<br>
1) Is it possible to average a certain event only if something else happened
after it? For example, let's say I have conditions 1 and 2. I want to average
each condition, but only when the trigger happened and I received a response
from the subject, which is coded as a <st1:metricconverter ProductID="3 in"
w:st="on">3 in</st1:metricconverter> the trigger line. In other words, average
all the occurrences of 1 or 2 only when there's a 3 after them. I wrote a
script to do that in Matlab using the MNE toolbox, but since then lots of
people have joined the lab and they are not very familiar with matlab, so I was
wondering if there was a way to do such average within MNE, either by using the
GUI or a combination of .ave and .eve files.<o:p></o:p></span></font></p>
</div>
</blockquote>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Unfortunately, there is no direct way to do conditional averaging in
mne_process_raw/mne_browse_raw (yet). However, the easiest way around this is
to output a text format event file a and manipulate this file so that new event
numbers are assigned to the events meeting the requested combinations. I guess
such a script could be even written in Excel.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br>
<o:p></o:p></span></font></p>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>2) Something else my script does is to average conditions across
different fif files. In the example above, I could have several fif files with
such events, and the final .fif averaged file would represent the averages
across all files. I imagine this is possible to do with the MNE software by
using the global average parameter. Is that correct? Is there a different way
to do it besides specifying a different .ave file for each of my raw .fif
files? It's usually not a problem to do that for only a couple .fif files, but
when there're about 10 different .fif files to be averaged, it starts to get a
little cumbersome to keep track of all the .ave files, which look very similar
except for the output parameter.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>You can, indeed, make a grand average file using mne_process_raw. You
can use the --saveavetag option to create the output file names automatically.
Also, if mne_process_raw runs out of ave file name names when processing the
raw files, the last one available will be used. If you use custom event files,
you can specify them on the command line (in version 2.6). <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Let's assume<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>my.ave is your averaging file<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>my1_raw.fif and my2_raw.fif are your raw data files<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>my1.eve and my2.eve are your event files<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>You can do <o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>mne_process_raw <other options> --raw my1_raw.fif --raw
my2_raw.fif --eve my1.eve --eve my2.eve --ave my.ave --saveavetag -ave --gave
my-gave.fif<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>This will produce the averages in my1-ave.fif and my2-ave.fif and log
files my1-ave.log and my2-ave.log independent of what is specifie in my.ave.
Also, the my1.eve and my2.eve override the event file specification (if any) in
my.ave.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>Similarly, the --savecovtag option can be used to generate the
noise-covariance calculation output file names.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>I hope this helps.<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'>- Matti<o:p></o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
<div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
</div>
<p class=MsoNormal style='margin-bottom:12.0pt'><font size=3
face="Times New Roman"><span style='font-size:12.0pt'><o:p> </o:p></span></font></p>
<div><span style='word-spacing:0px'><span style='word-spacing:0px'>
<div><span style='word-spacing:0px'>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>-------------</span></font><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;min-height: 14px'><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p> </o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>Matti
Hamalainen, Ph.D.</span></font><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>Athinoula
A. Martinos Center for Biomedical Imaging</span></font><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>Massachusetts
General Hospital</span></font><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>Building
149, 13th Street, Mailcode 149-2301</span></font><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>Charlestown,
MA 02129-2060</span></font><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>USA</span></font><font
size=1 color=black face=Helvetica><span style='font-size:9.0pt;font-family:
Helvetica;color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt;min-height: 14px'><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p> </o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=3 color=black
face=Helvetica><span style='font-size:12.0pt;font-family:Helvetica;color:black'>e-mail
<a href="mailto:msh@nmr.mgh.harvard.edu"
target="_blank">msh@nmr.mgh.harvard.edu</a></span></font><font size=1
color=black face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;
color:black'><o:p></o:p></span></font></p>
<p style='margin:0cm;margin-bottom:.0001pt'><font size=1 color=black
face=Helvetica><span style='font-size:9.0pt;font-family:Helvetica;color:black'><o:p> </o:p></span></font></p>
<p class=MsoNormal><font size=1 color=black face=Helvetica><span
style='font-size:9.0pt;font-family:Helvetica;color:black'><br>
<br>
<o:p></o:p></span></font></p>
</div>
</span></span>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'></span><o:p> </o:p></span></font></p>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><o:p> </o:p></span></font></p>
</div>
</div>
<p class=MsoNormal><font size=3 face="Times New Roman"><span style='font-size:
12.0pt'><br>
<br clear=all>
<br>
-- <br>
Gustavo Sudre<o:p></o:p></span></font></p>
</div>
</body>
</html>