[Mne_analysis] Error running make_forward_solution: Head<-->sensor transform not found
Eric Larson
larson.eric.d at gmail.com
Thu Nov 19 12:05:11 EST 2015
No problem, glad it's working. FYI the latest version is actually 0.10, so
feel free to upgrade to that if you want, too.
Eric
On Thu, 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:
>>
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>>> 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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>>> ------------------------------
>>>
>>> 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
>>> >
>>> >
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>>
>>
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