[Mne_analysis] Error running make_forward_solution: Head<-->sensor transform not found
Emily Stephen
emilyps14 at gmail.com
Thu Nov 19 12:48:44 EST 2015
Just submitted a pull request for the change (first pull request ever woo
hoo).
On Thu, Nov 19, 2015 at 12:28 PM, Alexandre Gramfort <
alexandre.gramfort at telecom-paristech.fr> wrote:
> indeed.
>
> PR welcome.
>
> You can also send us the fix by editing the file directly on github:
>
> https://github.com/mne-tools/mne-python/edit/master/doc/advanced_setup.rst
>
> thanks for your help
>
> Alex
>
>
> On Thu, Nov 19, 2015 at 6:24 PM, Emily Stephen <emilyps14 at gmail.com>
> wrote:
> > Hi Hari,
> >
> > Maybe it would be a good idea to update the website. I was using the
> wrong
> > python because of this page:
> > http://martinos.org/mne/stable/advanced_setup.html
> >
> > That page could also point Martinos users to the mailing list. Not sure
> who
> > would be able to make the change, but it would be helpful for new users.
> >
> > Emily
> >
> > On Thu, Nov 19, 2015 at 12:11 PM, Hari Bharadwaj <
> hari at nmr.mgh.harvard.edu>
> > wrote:
> >>
> >> Hi Emily,
> >> Thanks for bringing this to our attention...Anaconda is indeed the
> >> recommended distribution at the center and will likely be the only one
> >> available in the near future.. We are phasing out the others. Please
> join
> >> the Martinos Python mailing list (if not already subscribing) to get any
> >> updates on that front:
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/martinos-python
> >>
> >> Info about the current anaconda version is here (from mailing list
> >> archive):
> >>
> >>
> https://mail.nmr.mgh.harvard.edu/pipermail//martinos-python/2015-September/000048.html
> >>
> >>
> >> Hari
> >>
> >> Hari Bharadwaj
> >> Research Fellow,
> >> Martinos Center for Biomedical Imaging,
> >> Massachusetts General Hospital
> >> Charlestown, MA 02129
> >>
> >> hari at nmr.mgh.harvard.edu
> >> www.haribharadwaj.com
> >> Ph: 734-883-5954
> >>
> >> On Nov 19, 2015, at 11:34 AM, Emily Stephen <emilyps14 at gmail.com>
> wrote:
> >>
> >> I noticed that the default python distribution on the Martinos system
> was
> >> using MNE 0.8. Switched to the anaconda distribution which was using MNE
> >> 0.9.
> >>
> >> After working through some bugs related to the version change, I no
> longer
> >> get the error I reported before.
> >>
> >> Sorry for wasting your time!
> >>
> >> Emily
> >>
> >>
> >> On Wed, Nov 18, 2015 at 4:02 PM, Emily Stephen <emilyps14 at gmail.com>
> >> wrote:
> >>>
> >>> Update:
> >>>
> >>> (1) Re Hari's suggestion
> >>>
> >>> I tried converting the fif file to a hpts file using the C
> >>> implementation:
> >>> (from the shell)
> >>> mne_convert_dig_data --fif $SUBJECT.fif --hptsout $SUBJECT.hpts
> >>> --headcoord
> >>>
> >>> (from python)
> >>> digfile_hpts = op.join(subjects_dir, subject, subject + '.hpts')
> >>> montage = mne.channels.read_montage(digfile_hpts)
> >>> raw = mne.io.read_raw_brainvision(subjects_dir + subject + '/' +
> subject
> >>> + '.vhdr',
> >>> montage=montage, verbose=None,
> >>> preload=False)
> >>>
> >>> This raises a new error:
> >>> None of the sensors defined in the montage were found in the info
> >>> structure. Check the channel names.
> >>>
> >>> The channel names in the montage are of the form '0001' ... '0291',
> with
> >>> duplicated '0001' ... '0064' at the end. The channel names in the raw
> data
> >>> are of the form '01' ... '64'.
> >>>
> >>> I noticed that the first column in the .hpts file has 'eeg' for the
> last
> >>> 64 rows (vs 'cardinal', 'hpi', and 'extra' for the previous ones). This
> >>> first column isn't being used by read_montage, but I think it is what
> >>> distinguishes the eeg channel locations from the other digitizer info.
> >>>
> >>> I could manually change the channel names in the .hpts file to '01' ...
> >>> '64' for those rows, to match the channel names in the Brainvision
> file. Not
> >>> a pretty solution, but it might work.
> >>>
> >>> (2) Re Eric's comment
> >>>
> >>> I'd be happy to cut down the script/files. Where should I upload files?
> >>> I'm at Martinos, want to be sure to follow HIPAA etc.
> >>>
> >>> In the meantime, I've created an issue on github linking back to this
> >>> thread.
> >>>
> >>> Thanks,
> >>> Emily
> >>>
> >>> On Wed, Nov 18, 2015 at 8:44 AM,
> >>> <mne_analysis-request at nmr.mgh.harvard.edu> wrote:
> >>>>
> >>>> Send Mne_analysis mailing list submissions to
> >>>> mne_analysis at nmr.mgh.harvard.edu
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> >>>> than "Re: Contents of Mne_analysis digest..."
> >>>>
> >>>>
> >>>> Today's Topics:
> >>>>
> >>>> 1. Error running make_forward_solution: Head<-->sensor
> >>>> transform
> >>>> not found (Emily Stephen)
> >>>> 2. Re: Error running make_forward_solution: Head<-->sensor
> >>>> transform not found (Hari Bharadwaj)
> >>>> 3. Re: Error running make_forward_solution: Head<-->sensor
> >>>> transform not found (Eric Larson)
> >>>>
> >>>>
> >>>> ----------------------------------------------------------------------
> >>>>
> >>>> Message: 1
> >>>> Date: Tue, 17 Nov 2015 19:07:05 -0500
> >>>> From: Emily Stephen <emilyps14 at gmail.com>
> >>>> Subject: [Mne_analysis] Error running make_forward_solution:
> >>>> Head<-->sensor transform not found
> >>>> To: mne_analysis at nmr.mgh.harvard.edu
> >>>> Message-ID:
> >>>>
> >>>> <CAHgMKiV9thqbaSLYNU31jCZ4FCdUoYbraAUW3=+o4wM+CSBJqA at mail.gmail.com>
> >>>> Content-Type: text/plain; charset="utf-8"
> >>>>
> >>>>
> >>>> Hi All,
> >>>>
> >>>> I'm getting an error when I run mne.make_forward_solution, but only
> if I
> >>>> try to save the result.
> >>>>
> >>>> That is, if I set fname=None then the whole thing runs fine, but if I
> >>>> set
> >>>> fname=<filename>, it fails in the call to write_forward_solution with
> >>>> the
> >>>> error:
> >>>> Head<-->sensor transform not found
> >>>>
> >>>> Seems like write_forward_solution is expecting values in info under
> >>>> dev_head_t or ctf_head_t, which never got set.
> >>>>
> >>>> I think it may be related to the fact that I'm loading (just EEG) data
> >>>> from
> >>>> a brainvision file using mne.io.read_raw_brainvision.
> >>>>
> >>>> I've been struggling to figure out how to include the digitizer
> >>>> information
> >>>> in the preprocessed data. My digitizer info is in a .fif file that
> >>>> otherwise doesn't contain any measurement data (I can't even figure
> out
> >>>> how
> >>>> to load it using the python MNE). So far the only thing I've done with
> >>>> that
> >>>> file is to use it to update the channel locations with a call to the C
> >>>> implementation:
> >>>> call(['mne_check_eeg_locations',
> >>>> '--file', fname,
> >>>> '--dig', op.join(subjects_dir,subject,subject + '.fif'),
> >>>> '--fix'])
> >>>>
> >>>> I'm new to all of this (including python) so any help would be much
> >>>> appreciated! I've attached the code (apologies for the mess).
> >>>>
> >>>> Thanks,
> >>>> Emily
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> >>>>
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> >>>> -------------- next part --------------
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> >>>> Type: text/x-python-script
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> >>>> Desc: not available
> >>>> Url :
> >>>>
> http://mail.nmr.mgh.harvard.edu/pipermail/mne_analysis/attachments/20151117/e57b3044/attachment-0001.bin
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> Message: 2
> >>>> Date: Tue, 17 Nov 2015 22:13:03 -0500 (EST)
> >>>> From: "Hari Bharadwaj" <hari at nmr.mgh.harvard.edu>
> >>>> Subject: Re: [Mne_analysis] Error running make_forward_solution:
> >>>> Head<-->sensor transform not found
> >>>> To: "Discussion and support forum for the users of MNE Software"
> >>>> <mne_analysis at nmr.mgh.harvard.edu>
> >>>> Cc: mne_analysis at nmr.mgh.harvard.edu
> >>>> Message-ID:
> >>>>
> >>>> <51230.24.34.210.250.1447816383.squirrel at mail.nmr.mgh.harvard.edu>
> >>>> Content-Type: text/plain;charset=iso-8859-1
> >>>>
> >>>> Hi Emily,
> >>>> Perhaps you could try converting the digitization data to one of
> the
> >>>> formats (e.g., .hpts) accepted by mne.channels.read_montage(.) using
> >>>> the C-version of mne_convert_dig_data (if they are already not
> >>>> available in one of those formats). Once you do that and read it into
> >>>> python as a Montage object using mne.channels.read_montage(.), you
> >>>> could supply it as to the montage argument in
> >>>> mne.io.read_raw_brainvision(.).
> >>>>
> >>>> Also, the digitization data should contain cardinal points (like
> nasion,
> >>>> LPA, RAP) for the head along with the EEG sensor locations.. That way,
> >>>> "head coordinated" and "sensor coordinates" can be matched in the
> >>>> Montage.
> >>>>
> >>>> HTH,
> >>>> Hari
> >>>>
> >>>>
> >>>>
> >>>> On Tue, November 17, 2015 7:07 pm, Emily Stephen wrote:
> >>>> > Hi All,
> >>>> >
> >>>> > I'm getting an error when I run mne.make_forward_solution, but only
> if
> >>>> > I
> >>>> > try to save the result.
> >>>> >
> >>>> > That is, if I set fname=None then the whole thing runs fine, but if
> I
> >>>> > set
> >>>> > fname=<filename>, it fails in the call to write_forward_solution
> with
> >>>> > the
> >>>> > error:
> >>>> > Head<-->sensor transform not found
> >>>> >
> >>>> > Seems like write_forward_solution is expecting values in info under
> >>>> > dev_head_t or ctf_head_t, which never got set.
> >>>> >
> >>>> > I think it may be related to the fact that I'm loading (just EEG)
> data
> >>>> > from
> >>>> > a brainvision file using mne.io.read_raw_brainvision.
> >>>> >
> >>>> > I've been struggling to figure out how to include the digitizer
> >>>> > information
> >>>> > in the preprocessed data. My digitizer info is in a .fif file that
> >>>> > otherwise doesn't contain any measurement data (I can't even figure
> >>>> > out
> >>>> > how
> >>>> > to load it using the python MNE). So far the only thing I've done
> with
> >>>> > that
> >>>> > file is to use it to update the channel locations with a call to
> the C
> >>>> > implementation:
> >>>> > call(['mne_check_eeg_locations',
> >>>> > '--file', fname,
> >>>> > '--dig', op.join(subjects_dir,subject,subject + '.fif'),
> >>>> > '--fix'])
> >>>> >
> >>>> > I'm new to all of this (including python) so any help would be much
> >>>> > appreciated! I've attached the code (apologies for the mess).
> >>>> >
> >>>> > Thanks,
> >>>> > Emily
> >>>> > _______________________________________________
> >>>> > Mne_analysis mailing list
> >>>> > Mne_analysis at nmr.mgh.harvard.edu
> >>>> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>>
> >>>>
> >>>> --
> >>>> Hari Bharadwaj
> >>>> Research Fellow
> >>>> Martinos Center for Biomedical Imaging,
> >>>> Massachusetts General Hospital
> >>>> 149 Thirteenth Street,
> >>>> Charlestown, MA 02129
> >>>>
> >>>> hari at nmr.mgh.harvard.edu
> >>>> Ph: 734-883-5954
> >>>> www.haribharadwaj.com
> >>>>
> >>>>
> >>>> ------------------------------
> >>>>
> >>>> Message: 3
> >>>> Date: Wed, 18 Nov 2015 08:44:22 -0500
> >>>> From: Eric Larson <larson.eric.d at gmail.com>
> >>>> Subject: Re: [Mne_analysis] Error running make_forward_solution:
> >>>> Head<-->sensor transform not found
> >>>> To: Discussion and support forum for the users of MNE Software
> >>>> <mne_analysis at nmr.mgh.harvard.edu>
> >>>> Message-ID:
> >>>>
> >>>> <CAGu2niVt3EnAv1566f=JjFWXVBof-yrC09f0M_+NTs60mKrPrg at mail.gmail.com>
> >>>> Content-Type: text/plain; charset="utf-8"
> >>>>
> >>>> Can you simplify the script to use a minimal number of files and lines
> >>>> to
> >>>> reproduce the error (e.g., hopefully it doesn't depend on bad channels
> >>>> at
> >>>> all), and upload the necessary files and script somewhere? I guess
> that
> >>>> error could happen if you only have sensors in head coordinates to
> start
> >>>> with -- we can probably work around it.
> >>>>
> >>>> It shouldn't be too difficult to add that digitization information
> >>>> without
> >>>> having to resort to MNE-C tools. Feel free to open an mne-python issue
> >>>> about this stuff so we can hash out a solution, then we can report
> back
> >>>> to
> >>>> this thread.
> >>>>
> >>>> Eric
> >>>>
> >>>>
> >>>> On Tue, Nov 17, 2015 at 10:13 PM, Hari Bharadwaj
> >>>> <hari at nmr.mgh.harvard.edu>
> >>>> wrote:
> >>>>
> >>>> > Hi Emily,
> >>>> > Perhaps you could try converting the digitization data to one of
> >>>> > the
> >>>> > formats (e.g., .hpts) accepted by mne.channels.read_montage(.) using
> >>>> > the C-version of mne_convert_dig_data (if they are already not
> >>>> > available in one of those formats). Once you do that and read it
> into
> >>>> > python as a Montage object using mne.channels.read_montage(.), you
> >>>> > could supply it as to the montage argument in
> >>>> > mne.io.read_raw_brainvision(.).
> >>>> >
> >>>> > Also, the digitization data should contain cardinal points (like
> >>>> > nasion,
> >>>> > LPA, RAP) for the head along with the EEG sensor locations.. That
> way,
> >>>> > "head coordinated" and "sensor coordinates" can be matched in the
> >>>> > Montage.
> >>>> >
> >>>> > HTH,
> >>>> > Hari
> >>>>
> >>>> >
> >>>> >
> >>>> > On Tue, November 17, 2015 7:07 pm, Emily Stephen wrote:
> >>>> > > Hi All,
> >>>> > >
> >>>> > > I'm getting an error when I run mne.make_forward_solution, but
> only
> >>>> > > if I
> >>>> > > try to save the result.
> >>>> > >
> >>>> > > That is, if I set fname=None then the whole thing runs fine, but
> if
> >>>> > > I set
> >>>> > > fname=<filename>, it fails in the call to write_forward_solution
> >>>> > > with the
> >>>> > > error:
> >>>> > > Head<-->sensor transform not found
> >>>> > >
> >>>> > > Seems like write_forward_solution is expecting values in info
> under
> >>>> > > dev_head_t or ctf_head_t, which never got set.
> >>>> > >
> >>>> > > I think it may be related to the fact that I'm loading (just EEG)
> >>>> > > data
> >>>> > > from
> >>>> > > a brainvision file using mne.io.read_raw_brainvision.
> >>>> > >
> >>>> > > I've been struggling to figure out how to include the digitizer
> >>>> > > information
> >>>> > > in the preprocessed data. My digitizer info is in a .fif file that
> >>>> > > otherwise doesn't contain any measurement data (I can't even
> figure
> >>>> > > out
> >>>> > > how
> >>>> > > to load it using the python MNE). So far the only thing I've done
> >>>> > > with
> >>>> > > that
> >>>> > > file is to use it to update the channel locations with a call to
> the
> >>>> > > C
> >>>> > > implementation:
> >>>> > > call(['mne_check_eeg_locations',
> >>>> > > '--file', fname,
> >>>> > > '--dig', op.join(subjects_dir,subject,subject + '.fif'),
> >>>> > > '--fix'])
> >>>> > >
> >>>> > > I'm new to all of this (including python) so any help would be
> much
> >>>> > > appreciated! I've attached the code (apologies for the mess).
> >>>> > >
> >>>> > > Thanks,
> >>>> > > Emily
> >>>> > > _______________________________________________
> >>>> > > Mne_analysis mailing list
> >>>> > > Mne_analysis at nmr.mgh.harvard.edu
> >>>> > > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>>> >
> >>>> >
> >>>> > --
> >>>> > Hari Bharadwaj
> >>>> > Research Fellow
> >>>> > Martinos Center for Biomedical Imaging,
> >>>> > Massachusetts General Hospital
> >>>> > 149 Thirteenth Street,
> >>>> > Charlestown, MA 02129
> >>>> >
> >>>> > hari at nmr.mgh.harvard.edu
> >>>> > Ph: 734-883-5954
> >>>> > www.haribharadwaj.com
> >>>> > _______________________________________________
> >>>> > 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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> >>>> > in
> >>>> > error
> >>>> > but does not contain patient information, please contact the sender
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> >>>> > dispose of the e-mail.
> >>>> >
> >>>> >
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> >>>>
> >>>> ------------------------------
> >>>>
> >>>> _______________________________________________
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> >>>>
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> >>>> *******************************************
> >>>
> >>>
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
> >> _______________________________________________
> >> Mne_analysis mailing list
> >> Mne_analysis at nmr.mgh.harvard.edu
> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >>
> >>
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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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> in
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> >> but does not contain patient information, please contact the sender and
> >> properly
> >> dispose of the e-mail.
> >>
> >
> >
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> > Mne_analysis at nmr.mgh.harvard.edu
> > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis
> >
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