[Mne_analysis] No Isotrak data found in (raw .fif file)
dgw
dgwakeman at gmail.com
Mon Mar 12 15:09:45 EDT 2012
Hi Stephen,
It sounds like you actually, have two problems at the moment. The first
one we can solve now (I think...;)). I have noticed some strange
behavior in the stable version of MNE with "-trans.fif" files. I do not
think it can handle these files properly. What I recommend you do is:
start mne_analyze
use the "good" fif file (the one with the HPI) to load the digitization
points
do the coordinate alignment
Then save the "MRI set"
(At this point, I like to go in and rename this file, because I find the
default naming difficult to keep track of (previous versions allowed
custom naming)). If you want to do this use:
mv $SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets/<name of the newest
file>$SUBJECTS_DIR/$SUBJECT/mri/T1-neuromag/sets/<your preferred name>.fif
then use mne_do_forward_solution with --mri <your preferred name>.fif
. do not use --mricoord.
This should work
The second problem is your average file, The following trick may work.
Try putting the file with HPI data first in the list of files you use
for averaging i.e. the first --raw file (obviously change the order of
.ave & .cov files as well). I believe MNE will take the first file's
data for the HPI information.
Also, if these don't work. Try providing more information about your
MATLAB difficulties for assistance (this code should be working, though
your raw data problems may require some additional code to be added to
add in missing information).
HTH
D
Stephen Politzer-Ahles wrote:
> 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 <mailto: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 <http://r2.info>['dig']=raw.info <http://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>
> <mailto: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><__mailto: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>
> <mailto: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><__mailto: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><mailto:krie__gerd 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><tel:%28412%29648-9654>
> >> __________________________________
> >> From:
> mne_analysis-bounces at nmr.mgh.__harvard.edu
> <mailto:mne_analysis-bounces at nmr.mgh.harvard.edu>
>
> <mailto: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>
>
> <mailto: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>
> <mailto: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>
> <mailto: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
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> <mailto: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
> <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
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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>
> <mailto: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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> >
> >
> > 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
> <http://www.partners.org/complianceline> . If the e-mail
> was sent to you in
> > error
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>
>
> -- 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
> contains patient information, please contact the
> Partners
> Compliance HelpLine at
> http://www.partners.org/__complianceline
> <http://www.partners.org/complianceline> . If the e-mail was
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>
>
>
> --
> 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
> contains patient information, please contact the Partners
> Compliance HelpLine at
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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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