[Mne_analysis] No Isotrak data found in (raw .fif file)
dgw
dgwakeman at gmail.com
Fri Mar 9 15:12:54 EST 2012
This is also possible with the MATLAB toolbox. Read both files into
MATLAB, copy the relevant transformation data and write the formerly
deficient file. see mne_ex_read_write_raw, for help with the basics.
If you are of the Python persuasion, I suspect there is support for that
too (Martin Alex?)
D
Stephen Politzer-Ahles wrote:
> Hi Jon,
>
> Thanks for the suggestion. Unfortunately I don't have Neuromag here; my
> data are from CTF.
>
> Best,
> Steve
>
> On Fri, Mar 9, 2012 at 11:27 AM, Jon Houck <jhouck at unm.edu
> <mailto:jhouck at unm.edu>> wrote:
>
> 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 <mailto: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
> <mailto: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 <mailto: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 <mailto: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 <tel:%28412%29648-9654>
> >> ________________________________
> >> From: mne_analysis-bounces at nmr.mgh.harvard.edu
> <mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>
> >> [mne_analysis-bounces at nmr.mgh.harvard.edu
> <mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>] on behalf
> of Stephen
> >> Politzer-Ahles [politzerahless at gmail.com
> <mailto:politzerahless at gmail.com>]
> >> Sent: Tuesday, March 06, 2012 3:51 PM
> >> To: mne_analysis at nmr.mgh.harvard.edu
> <mailto: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
> <mailto: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
> <mailto: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
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> > error
> > but does not contain patient information, please contact
> the sender and
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> >
>
>
>
>
> --
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/
>
> _______________________________________________
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> Mne_analysis at nmr.mgh.harvard.edu
> <mailto: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
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> 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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> 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
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