[Mne_analysis] No Isotrak data found in (raw .fif file)

[Stephen Politzer-Ahles]

Donald and Alexandre,

Thanks for the suggestions. I was indeed able to find another run of this
same participant that still has the digitization data. I imported the raw
data into MNE and then used that, rather than my original .fif file, for
loading digitization points when I did co-registration; then I saved the
co-registration, renamed it so that it matched what it would have been if I
used the original file (subj006_raw-trans.fif), and then tried doing
forward and inverse solutions. At mne_setup_forward_solution I got the
following error:

MEG -> head coordinate transformation not found

I haven't gotten that error with other subjects so I assume it must have
something to do with my messing around with the filenames? I tried changing
the filenames at several different stages but still keep getting the error.
Is there a better way to do this? (For instance, Alexandre, if I understand
your suggestion right, should I be adding the digitization points from the
good .fif file directly into the bad _raw.fif file and then using that one
to load digitization data when I do coregistration?)

Thanks again,
Steve


On Thu, Mar 8, 2012 at 10:55 AM, Alexandre Gramfort <
gramfort at nmr.mgh.harvard.edu> wrote:

> Hi Stephen,
>
> if you have the digitization points in one of the fif files for this
> particular subject than we can add them to a raw file or you can load
> them directly in mne_analyze. Otherwise I'm afraid you'll have to  do
> the coregistration only using the 3 fiducials which is fairly
> imprecise.
>
> Alex
>
> On Thu, Mar 8, 2012 at 4:25 PM, Stephen Politzer-Ahles
> <politzerahless at gmail.com> wrote:
> > Hi Donald,
> >
> > 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:
> >
> >        104 = {    107 = isotrak
> >           213 = dig. point [5]
> >        105 = }    107 = isotrak
> >        104 = {    109 = HPI result
> >           213 = dig. point [3]
> >           222 = transform [2]
> >        105 = }    109 = HPI result
> >
> > 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).
> >
> > Thanks again,
> > Steve
> >
> >
> > On Tue, Mar 6, 2012 at 2:54 PM, Krieger, Donald N. <kriegerd at upmc.edu>
> > wrote:
> >>
> >> Hi Steve,
> >>
> >> 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.
> >>
> >> Don
> >>
> >> Don Krieger, Ph.D., D.ABNM
> >> Department of Neurological Surgery
> >> University of Pittsburgh
> >> (412)648-9654
> >> ________________________________
> >> From: mne_analysis-bounces at nmr.mgh.harvard.edu
> >> [mne_analysis-bounces at nmr.mgh.harvard.edu] on behalf of Stephen
> >> Politzer-Ahles [politzerahless at gmail.com]
> >> Sent: Tuesday, March 06, 2012 3:51 PM
> >> To: mne_analysis at nmr.mgh.harvard.edu
> >> Subject: [Mne_analysis] No Isotrak data found in (raw .fif file)
> >>
> >> Hello MNEers,
> >>
> >> 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:
> >>
> >> No Isotrak data found in (the name of the .fif file)
> >>
> >> 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.
> >>
> >> Does anyone have any idea what might be causing this error and how to
> fix
> >> it?
> >>
> >> Best,
> >> Steve Politzer-Ahles
> >>
> >> --
> >> Stephen Politzer-Ahles
> >> University of Kansas
> >> Linguistics Department
> >> http://www.linguistics.ku.edu/
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >> The information in this e-mail is intended only for the person to whom
> it
> >> is
> >> addressed. If you believe this e-mail was sent to you in error and the
> >> e-mail
> >> contains patient information, please contact the Partners Compliance
> >> HelpLine at
> >> http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> >> error
> >> but does not contain patient information, please contact the sender and
> >> properly
> >> dispose of the e-mail.
> >>
> >
> >
> >
> > --
> > Stephen Politzer-Ahles
> > University of Kansas
> > Linguistics Department
> > http://www.linguistics.ku.edu/
> >
> > _______________________________________________
> > Mne_analysis mailing list
> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
> >
> > The information in this e-mail is intended only for the person to whom
> it is
> > addressed. If you believe this e-mail was sent to you in error and the
> > e-mail
> > contains patient information, please contact the Partners Compliance
> > HelpLine at
> > http://www.partners.org/complianceline . If the e-mail was sent to you
> in
> > error
> > but does not contain patient information, please contact the sender and
> > properly
> > dispose of the e-mail.
> >
>



-- 
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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