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

Stephen Politzer-Ahles politzerahless at gmail.com
Fri Mar 9 15:09:43 EST 2012
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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> 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> 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
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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
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>>> > but does not contain patient information, please contact the sender and
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>>> > dispose of the e-mail.
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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/
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