[Mne_analysis] No Isotrak data found in (raw .fif file)
Manfred G Kitzbichler
manfredg at nmr.mgh.harvard.edu
Fri Mar 9 16:55:39 EST 2012
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>> 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/
>> >>
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>> >
>> > --
>> > Stephen Politzer-Ahles
>> > University of Kansas
>> > Linguistics Department
>> > http://www.linguistics.ku.edu/
>> >
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>>
>>
>> --
>> Stephen Politzer-Ahles
>> University of Kansas
>> Linguistics Department
>> http://www.linguistics.ku.edu/
>>
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>>
>>
>>
>>
>>
>>
>> --
>> Stephen Politzer-Ahles
>> University of Kansas
>> Linguistics Department
>> http://www.linguistics.ku.edu/
>>
>>
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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
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