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

dgw dgwakeman at gmail.com
Fri Mar 9 15:12:54 EST 2012
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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
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>              >> is
>              >> addressed. If you believe this e-mail was sent to you in
>             error and the
>              >> e-mail
>              >> contains patient information, please contact the
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>              >>
>              >
>              >
>              >
>              > --
>              > Stephen Politzer-Ahles
>              > University of Kansas
>              > Linguistics Department
>              > http://www.linguistics.ku.edu/
>              >
>              > _______________________________________________
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>              >
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>              >
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>              > addressed. If you believe this e-mail was sent to you in
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>              > e-mail
>              > contains patient information, please contact the Partners
>             Compliance
>              > HelpLine at
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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
>         <mailto:Mne_analysis at nmr.mgh.harvard.edu>
>         https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> 
> 
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> 
> 
> 
> 
> 
> 
> 
> 
> 
> -- 
> Stephen Politzer-Ahles
> University of Kansas
> Linguistics Department
> http://www.linguistics.ku.edu/
> 
> 
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