[Mne_analysis] No Isotrak data found in (raw .fif file)
Stephen Politzer-Ahles
politzerahless at gmail.com
Mon Mar 12 14:52:56 EDT 2012
Hi Alex,
Thanks for your suggestion. Yes, I meant mne_do_forward_solution, sorry
about that!
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):
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
I also tried passing the good trans.fif in using the --trans option:
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
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.
Do you have any other ideas how to pass the good trans.fif file in? I
assume I must be missing something obvious :)
Best,
Steve
On Fri, Mar 9, 2012 at 2:26 PM, Alexandre Gramfort <
gramfort at nmr.mgh.harvard.edu> wrote:
> hi steve,
>
> > 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 assume you mean mne_do_forward_solution
>
> if it's the case then you can explicitly pass the trans.fif file with
> the --mricoord option.
>
> let me know if it works. Otherwise you can the dig points to the raw
> file with Python.
>
> Alex
>
> > 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
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> >> >> error
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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
> >> > 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/
>
--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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