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

Jon Houck jhouck at unm.edu
Fri Mar 9 12:27:03 EST 2012
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Hi Steve,

If the Neuromag software is available, you can use the utility
copy_trans_fiff to copy the head transformation from the good file onto the
bad file.

Jon






On Fri, Mar 9, 2012 at 10:09 AM, Stephen Politzer-Ahles <
politzerahless at gmail.com> wrote:

> 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
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>> >>
>> >
>> >
>> >
>> > --
>> > Stephen Politzer-Ahles
>> > University of Kansas
>> > Linguistics Department
>> > http://www.linguistics.ku.edu/
>> >
>> > _______________________________________________
>> > Mne_analysis mailing list
>> > Mne_analysis at nmr.mgh.harvard.edu
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>
>
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/
>
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> Mne_analysis mailing list
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>
> 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
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