Hi Alex,<br><br>Thanks for your suggestion. Yes, I meant mne_do_forward_solution, sorry about that!<br><br>Explicitly passing the good trans.fif file would definitely be the easiest option for me. But are you sure --mricoord is the option for that? When I checked the manual it said this is just an option that can be turned on to do computations in the MRI coordinate system (rather than a parameter that I can pass a filename to). Just in case, I tried it out, but still got the error (in this, "subj006" is my bad file and "subj006_auditory" is the good run from the same subject):<br>
<br>mne_do_forward_solution --mindist 5 --meas $SAMPLE/MEG/subj006/subj006_ave.fif --bem subj006-5120-bem-sol.fif --megonly --mricoord subj006_auditory_raw-trans.fif<br><br>I also tried passing the good trans.fif in using the --trans option:<br>
<br>mne_do_forward_solution --mindist 5 --meas
$SAMPLE/MEG/subj006/subj006_ave.fif --bem subj006-5120-bem-sol.fif
--megonly --trans subj006_auditory_raw-trans.fif<br><br>which also didn't work--according to the manual --trans expects a text file containing a 4x4 matrix, and I don't think that's what's in the trans.file? I tried making my own text file by just typing in the values from the rotation matrix that I see when manually doing the MEG-MRI coordinate alignment, but that didn't work either. <br>
<br>Do you have any other ideas how to pass the good trans.fif file in? I assume I must be missing something obvious :)<br><br>Best,<br>Steve<br><br><br><div class="gmail_quote">On Fri, Mar 9, 2012 at 2:26 PM, Alexandre Gramfort <span dir="ltr"><<a href="mailto:gramfort@nmr.mgh.harvard.edu">gramfort@nmr.mgh.harvard.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">hi steve,<br>
<div class="im"><br>
> Thanks for the suggestions. I was indeed able to find another run of this<br>
> same participant that still has the digitization data. I imported the raw<br>
> data into MNE and then used that, rather than my original .fif file, for<br>
> loading digitization points when I did co-registration; then I saved the<br>
> co-registration, renamed it so that it matched what it would have been if I<br>
> used the original file (subj006_raw-trans.fif), and then tried doing forward<br>
> and inverse solutions. At mne_setup_forward_solution I got the following<br>
> error:<br>
><br>
> MEG -> head coordinate transformation not found<br>
<br>
</div>I assume you mean mne_do_forward_solution<br>
<br>
if it's the case then you can explicitly pass the trans.fif file with<br>
the --mricoord option.<br>
<br>
let me know if it works. Otherwise you can the dig points to the raw<br>
file with Python.<br>
<br>
Alex<br>
<div class="HOEnZb"><div class="h5"><br>
> I haven't gotten that error with other subjects so I assume it must have<br>
> something to do with my messing around with the filenames? I tried changing<br>
> the filenames at several different stages but still keep getting the error.<br>
> Is there a better way to do this? (For instance, Alexandre, if I understand<br>
> your suggestion right, should I be adding the digitization points from the<br>
> good .fif file directly into the bad _raw.fif file and then using that one<br>
> to load digitization data when I do coregistration?)<br>
><br>
> Thanks again,<br>
> Steve<br>
><br>
><br>
><br>
> On Thu, Mar 8, 2012 at 10:55 AM, Alexandre Gramfort<br>
> <<a href="mailto:gramfort@nmr.mgh.harvard.edu">gramfort@nmr.mgh.harvard.edu</a>> wrote:<br>
>><br>
>> Hi Stephen,<br>
>><br>
>> if you have the digitization points in one of the fif files for this<br>
>> particular subject than we can add them to a raw file or you can load<br>
>> them directly in mne_analyze. Otherwise I'm afraid you'll have to do<br>
>> the coregistration only using the 3 fiducials which is fairly<br>
>> imprecise.<br>
>><br>
>> Alex<br>
>><br>
>> On Thu, Mar 8, 2012 at 4:25 PM, Stephen Politzer-Ahles<br>
>> <<a href="mailto:politzerahless@gmail.com">politzerahless@gmail.com</a>> wrote:<br>
>> > Hi Donald,<br>
>> ><br>
>> > Thanks for the suggestion. I was able to do this using mne_show_fiff and<br>
>> > there are indeed differences in the tags. I've attached text copies of<br>
>> > the<br>
>> > output of mne_show_fiff for the subject I'm getting the error for<br>
>> > (subj006)<br>
>> > and a good one (subj023). The difference seems to be that the bad<br>
>> > subject's<br>
>> > 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<br>
>> > don't know why they're missing (but I have e-mailed the person who runs<br>
>> > our<br>
>> > MEG machine to see if she can tell).<br>
>> ><br>
>> > Thanks again,<br>
>> > Steve<br>
>> ><br>
>> ><br>
>> > On Tue, Mar 6, 2012 at 2:54 PM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu">kriegerd@upmc.edu</a>><br>
>> > wrote:<br>
>> >><br>
>> >> Hi Steve,<br>
>> >><br>
>> >> You might just look at the tags in the file using the Elekta tool:<br>
>> >> show_fiff . There's probably an mne or mne matlab toolbox tool which<br>
>> >> 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><br>
>> >> [<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a>] on behalf of Stephen<br>
>> >> 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)<br>
>> >><br>
>> >> Hello MNEers,<br>
>> >><br>
>> >> While doing MRI-MEG co-registration, for one particular subject when I<br>
>> >> open mne_analyze and try to Load Digitizer Data from the raw .fif file,<br>
>> >> I<br>
>> >> 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<br>
>> >> processed<br>
>> >> them all the same way using a batch. Just now I tried re-doing some of<br>
>> >> the<br>
>> >> processing for this subject (epoching, artifact rejection, and<br>
>> >> filtering had<br>
>> >> already been done in CTF, but I redid the import to .fif, averaging,<br>
>> >> and<br>
>> >> 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<br>
>> >> fix<br>
>> >> 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><br>
>> >><br>
>> >> _______________________________________________<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<br>
>> >> it<br>
>> >> is<br>
>> >> addressed. If you believe this e-mail was sent to you in error and the<br>
>> >> e-mail<br>
>> >> contains patient information, please contact the Partners Compliance<br>
>> >> 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<br>
>> >> in<br>
>> >> error<br>
>> >> but does not contain patient information, please contact the sender and<br>
>> >> properly<br>
>> >> dispose of the e-mail.<br>
>> >><br>
>> ><br>
>> ><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><br>
>> ><br>
>> > _______________________________________________<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<br>
>> > it is<br>
>> > addressed. If you believe this e-mail was sent to you in error and the<br>
>> > e-mail<br>
>> > contains patient information, please contact the Partners Compliance<br>
>> > 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<br>
>> > in<br>
>> > error<br>
>> > but does not contain patient information, please contact the sender and<br>
>> > properly<br>
>> > dispose of the e-mail.<br>
>> ><br>
><br>
><br>
><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><br>
</div></div></blockquote></div><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><br>