<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:st2="isiresearchsoft-com/cwyw" xmlns="http://www.w3.org/TR/REC-html40" xmlns:ns0="urn:schemas-microsoft-com:office:smarttags">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
<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="PlaceName" /><o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PlaceType" /><o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="place" /><o:SmartTagType namespaceuri="isiresearchsoft-com/cwyw" name="citation" /><o:SmartTagType namespaceuri="urn:schemas-microsoft-com:office:smarttags" name="PersonName" /><!--[if !mso]>
<style>
st1\:*{behavior:url(#default#ieooui) }st2\:*{behavior:url(#default#ieooui) }
</style>
<![endif]--><style>
<!--
/* Font Definitions */
@font-face
{font-family:Batang;
panose-1:2 3 6 0 0 1 1 1 1 1;}
@font-face
{font-family:Tahoma;
panose-1:2 11 6 4 3 5 4 4 2 4;}
@font-face
{font-family:"\@Batang";
panose-1:0 0 0 0 0 0 0 0 0 0;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0in;
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;}
span.EmailStyle17
{mso-style-type:personal-reply;
font-family:Arial;
color:navy;}
@page Section1
{size:8.5in 11.0in;
margin:1.0in 1.25in 1.0in 1.25in;}
div.Section1
{page:Section1;}
-->
</style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-US" link="blue" vlink="blue">
<div class="Section1">
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Hi Steve,<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span 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 style="font-size:
10.0pt;font-family:Arial;color:navy">There are two pieces to this problem. If the tags are truly missing from the file, that means that you are lacking key information that
you need for the thumb-fingered frameless stereotaxis that we use to register the MEG measures with the volunteer’s brain. (1) If the data collected from this volunteer was done in a single acquisition run so that it’s all in a single file, it may well be
impossible to recover the necessary information. If the data was collected in more than one run and therefore resides in more than one file, you can in theory use the localization information from one of the files which contains it for the one which does
not. That information will necessarily have less reliability for the file which lacks it, but it’s probably pretty close.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span 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 style="font-size:
10.0pt;font-family:Arial;color:navy">If the former is the case, i.e. the data is in a single file, then you lack critical information and it’s lost. You can still use the
data for sensor space analysis but not for source space since you lack registration information. (2) If the latter is the case, i.e. the data is in multiple files and at least one of them contains the localization info, there’s likely a way to trick mne or
whatever other analysis tool you’re using to use the localization from one file while analyzing the other. Alternatively you may have to write something which creates a new .fif using the data from one file and the localization info from another. It’s a
sure thing that Matti or someone in his group can point you in the right direction for that.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span 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 style="font-size:
10.0pt;font-family:Arial;color:navy">P.S. I looked at the show_fiff output that you included and it does appear that the subject006 data lacks the localization stuff. Somebody
likely pushed the wrong button when going through the HPCI digitization. But try show_fiff –v just to be sure that you’re not missing something. That will show not only the tag names but what their values are.<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span 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 style="font-size:
10.0pt;font-family:Arial;color:navy">Don</span></font><font color="navy"><span style="color:navy"><o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="3" color="navy" face="Times New Roman"><span style="font-size:12.0pt;color:navy"> <o:p></o:p></span></font></p>
<p class="MsoNormal"><st1:PersonName w:st="on"><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">Don Krieger</span></font></st1:PersonName><font size="2" color="navy" face="Arial"><span style="font-size:10.0pt;font-family:Arial;color:navy">,
Ph.D., D.ABNM<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">Department of Neurological Surgery<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="2" face="Arial"><span style="font-size:10.0pt;
font-family:Arial"><ns0:place w:insAuthor="Donald N. Krieger" w:insDate="2012-03-08T10:28:00Z" w:endInsAuthor="Donald N. Krieger" w:endInsDate="2012-03-08T10:28:00Z"><ns0:PlaceType w:insAuthor="Donald N. Krieger" w:insDate="2012-03-08T10:28:00Z" w:endInsAuthor="Donald N. Krieger" w:endInsDate="2012-03-08T10:28:00Z"><st1:place w:st="on"><st1:PlaceType w:st="on"><font color="navy"><span style="color:navy">University</span></font></st1:PlaceType></ns0:PlaceType></st1:place><font color="navy"><span style="color:navy">
of </span></font><ns0:PlaceName w:insAuthor="Donald N. Krieger" w:insDate="2012-03-08T10:28:00Z" w:endInsAuthor="Donald N. Krieger" w:endInsDate="2012-03-08T10:28:00Z"><st1:PlaceName w:st="on"><font color="navy"><span style="color:navy">Pittsburgh</span></font></st1:PlaceName></ns0:PlaceName></ns0:place><font color="navy"><span style="color:navy"><o:p></o:p></span></font></span></font></p>
<p class="MsoNormal"><font size="2" color="navy" face="Arial"><span style="font-size:
10.0pt;font-family:Arial;color:navy">(412)648-9654</span></font><o:p></o:p></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">From:</span></font></b><font size="2" face="Tahoma"><span style="font-size:10.0pt;font-family:Tahoma"> Stephen Politzer-Ahles [mailto:politzerahless@gmail.com]
<br>
<b><span style="font-weight:bold">Sent:</span></b> Thursday, March 08, 2012 10:26 AM<br>
<b><span style="font-weight:bold">To:</span></b> Krieger, Donald N.<br>
<b><span style="font-weight:bold">Cc:</span></b> mne_analysis@nmr.mgh.harvard.edu<br>
<b><span style="font-weight:bold">Subject:</span></b> Re: [Mne_analysis] No Isotrak data found in (raw .fif file)</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">Hi Donald,<br>
<br>
Thanks for the suggestion. I was able to do this using mne_show_fiff and there are indeed differences in the tags. I've attached text copies of the output of mne_show_fiff for the subject I'm getting the error for (subj006) and a good one (subj023). The difference
seems to be that the bad subject's fiff is missing these tags that are present in other subjects' files:<br>
<br>
104 = { 107 = isotrak<br>
213 = dig. point [5]<br>
105 = } 107 = isotrak<br>
104 = { 109 = HPI result<br>
213 = dig. point [3]<br>
222 = transform [2]<br>
105 = } 109 = HPI result<br>
<br>
Is there a way to add these tags into the .fif file for that subject? I don't know why they're missing (but I have e-mailed the person who runs our MEG machine to see if she can tell).<br>
<br>
Thanks again,<br>
Steve<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, Mar 6, 2012 at 2:54 PM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu">kriegerd@upmc.edu</a>> wrote:<o:p></o:p></span></font></p>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt">Hi Steve,<br>
<br>
You might just look at the tags in the file using the Elekta tool: show_fiff . There's probably an mne or mne matlab toolbox tool which enables this too.<br>
<br>
Don<br>
<br>
Don Krieger, Ph.D., D.ABNM<br>
Department of Neurological Surgery<br>
University of Pittsburgh<br>
<a href="tel:%28412%29648-9654" value="+14126489654">(412)648-9654</a><br>
________________________________<br>
From: <a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a>] on behalf of Stephen Politzer-Ahles [<a href="mailto:politzerahless@gmail.com">politzerahless@gmail.com</a>]<br>
Sent: Tuesday, March 06, 2012 3:51 PM<br>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu">mne_analysis@nmr.mgh.harvard.edu</a><br>
Subject: [Mne_analysis] No Isotrak data found in (raw .fif file)<o:p></o:p></span></font></p>
<div>
<div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt"><br>
Hello MNEers,<br>
<br>
While doing MRI-MEG co-registration, for one particular subject when I open mne_analyze and try to Load Digitizer Data from the raw .fif file, I get this error:<br>
<br>
No Isotrak data found in (the name of the .fif file)<br>
<br>
I haven't gotten this error for any of my other subjects, and I processed them all the same way using a batch. Just now I tried re-doing some of the processing for this subject (epoching, artifact rejection, and filtering had already been done in CTF, but I
redid the import to .fif, averaging, and noise covariance matrix), and still got the same problem.<br>
<br>
Does anyone have any idea what might be causing this error and how to fix it?<br>
<br>
Best,<br>
Steve Politzer-Ahles<br>
<br>
--<br>
Stephen Politzer-Ahles<br>
University of Kansas<br>
Linguistics Department<br>
<a href="http://www.linguistics.ku.edu/" target="_blank">http://www.linguistics.ku.edu/</a><o:p></o:p></span></font></p>
</div>
</div>
<p class="MsoNormal" style="margin-bottom:12.0pt"><font size="3" face="Times New Roman"><span style="font-size:12.0pt">_______________________________________________<br>
Mne_analysis mailing list<br>
<a href="mailto:Mne_analysis@nmr.mgh.harvard.edu">Mne_analysis@nmr.mgh.harvard.edu</a><br>
<a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
<br>
<br>
The information in this e-mail is intended only for the person to whom it is<br>
addressed. If you believe this e-mail was sent to you in error and the e-mail<br>
contains patient information, please contact the Partners Compliance HelpLine at<br>
<a href="http://www.partners.org/complianceline" target="_blank">http://www.partners.org/complianceline</a> . If the e-mail was sent to you in error<br>
but does not contain patient information, please contact the sender and properly<br>
dispose of the e-mail.<o:p></o:p></span></font></p>
</div>
<p class="MsoNormal"><font size="3" face="Times New Roman"><span style="font-size:
12.0pt"><br>
<br clear="all">
<br>
-- <br>
Stephen Politzer-Ahles<br>
University of Kansas<br>
Linguistics Department<br>
<a href="http://www.linguistics.ku.edu/">http://www.linguistics.ku.edu/</a><o:p></o:p></span></font></p>
</div>
</body>
</html>