[Mne_analysis] No Isotrak data found in (raw .fif file)
Stephen Politzer-Ahles
politzerahless at gmail.com
Mon Mar 12 14:58:15 EDT 2012
Thanks for the suggestions, Dan and Manfred. I have not used MNE's MATLAB
toolbox or mne-python before (when I tried this weekend, I got problems
with the channel list in mne_ex_read_write_raw in MATLAB, and I won't be
able to get mne-python installed until my sysadmin can give me a hand
within installing Numpy and Scipy), but if I'm not able to solve the
problem using Alexandre's suggestion about mne_do_forward_solution then I
will continue working on those other solutions and let you know if I run
into further difficulties.
Thanks again,
Steve
On Fri, Mar 9, 2012 at 3:55 PM, Manfred G Kitzbichler <
manfredg at nmr.mgh.harvard.edu> wrote:
> Hi Stephen, Dan et al.
>
>
> On 03/09/2012 03:12 PM, dgw wrote:
>
>> 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
>>
>
> As for that last suggestion, that's exactly what I am doing with my data
> which has the same problem - maxfilter for some reason strips the isotrak
> data from the files. So I put it back in with mne-python simply using the
> commands:
>
> raw=mne.fiff.Raw(fn)
> r2=mne.fiff.Raw(fn2)
> r2.info['dig']=raw.info['dig']
> r2.save(fn3)
>
> where fn[123] are the input and output filenames respectively.
>
> Good luck,
>
> Manfred
>
>
>
>
>
>> 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<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<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 <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:krie**gerd at upmc.edu<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<mne_analysis-bounces at nmr.mgh.harvard.edu>
>>> <mailto:mne_analysis-bounces@**nmr.mgh.harvard.edu<mne_analysis-bounces at nmr.mgh.harvard.edu>
>>> >
>>> >> [mne_analysis-bounces at nmr.mgh.**harvard.edu<mne_analysis-bounces at nmr.mgh.harvard.edu>
>>> <mailto:mne_analysis-bounces@**nmr.mgh.harvard.edu<mne_analysis-bounces at nmr.mgh.harvard.edu>>]
>>> on behalf
>>> of Stephen
>>> >> Politzer-Ahles [politzerahless at gmail.com
>>> <mailto:politzerahless at gmail.**com<politzerahless at gmail.com>
>>> >]
>>> >> Sent: Tuesday, March 06, 2012 3:51 PM
>>> >> To: mne_analysis at nmr.mgh.harvard.**edu<mne_analysis at nmr.mgh.harvard.edu>
>>> <mailto:mne_analysis at nmr.mgh.**harvard.edu<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<Mne_analysis at nmr.mgh.harvard.edu>
>>> <mailto:Mne_analysis at nmr.mgh.**harvard.edu<Mne_analysis at nmr.mgh.harvard.edu>
>>> >
>>> >>
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>>> analysis<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/
>>> >
>>> > ______________________________**_________________
>>> > Mne_analysis mailing list
>>> > Mne_analysis at nmr.mgh.harvard.**edu<Mne_analysis at nmr.mgh.harvard.edu>
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>>> analysis<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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>>> Mne_analysis mailing list
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>>>
>>> --
>>> Stephen Politzer-Ahles
>>> University of Kansas
>>> Linguistics Department
>>> http://www.linguistics.ku.edu/
>>>
>>>
>>> ------------------------------**------------------------------**
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>>> 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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>>
>
> --
> Manfred G. Kitzbichler
> Martinos Center for Biomedical Imaging
> Dept of Neurology, Mass General Hospital
> 149 Thirteenth Street, Rm 10.018
> Charlestown, MA 02129, USA
>
>
>
--
Stephen Politzer-Ahles
University of Kansas
Linguistics Department
http://www.linguistics.ku.edu/
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