<div dir="ltr"><p>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.</p>
<p>After working through some bugs related to the version change, I no longer get the error I reported before. </p>
<p>Sorry for wasting your time!</p><p>Emily<br></p><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 4:02 PM, Emily Stephen <span dir="ltr"><<a href="mailto:emilyps14@gmail.com" target="_blank">emilyps14@gmail.com</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr"><div><div><div><div><div><div>Update:<br><br></div><div>(1) Re Hari's suggestion<br><br></div>I tried converting the fif file to a hpts file using the C implementation:<br></div>(from the shell)<br>mne_convert_dig_data --fif $SUBJECT.fif --hptsout $SUBJECT.hpts --headcoord<br><br></div>(from python)<br>digfile_hpts = op.join(subjects_dir, subject, subject + '.hpts')<br>montage = mne.channels.read_montage(digfile_hpts)<br>raw = mne.io.read_raw_brainvision(subjects_dir + subject + '/' + subject + '.vhdr',<br> montage=montage, verbose=None, preload=False)<br><br></div>This raises a new error:<br>None of the sensors defined in the montage were found in the info structure. Check the channel names.<br><br></div>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'.<br><br></div><div>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.<br><br></div><div>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.<br><br></div><div>(2) Re Eric's comment<br><br></div><div>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. <br><br></div><div>In the meantime, I've created an issue on github linking back to this thread.<br><br></div><div>Thanks,<br></div>Emily<div class="gmail_extra"><br><div class="gmail_quote">On Wed, Nov 18, 2015 at 8:44 AM, <span dir="ltr"><<a href="mailto:mne_analysis-request@nmr.mgh.harvard.edu" target="_blank">mne_analysis-request@nmr.mgh.harvard.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">Send Mne_analysis mailing list submissions to<br>
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Today's Topics:<br>
<br>
1. Error running make_forward_solution: Head<-->sensor transform<br>
not found (Emily Stephen)<br>
2. Re: Error running make_forward_solution: Head<-->sensor<br>
transform not found (Hari Bharadwaj)<br>
3. Re: Error running make_forward_solution: Head<-->sensor<br>
transform not found (Eric Larson)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Tue, 17 Nov 2015 19:07:05 -0500<br>
From: Emily Stephen <<a href="mailto:emilyps14@gmail.com" target="_blank">emilyps14@gmail.com</a>><br>
Subject: [Mne_analysis] Error running make_forward_solution:<span class=""><br>
Head<-->sensor transform not found<br></span>
To: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<CAHgMKiV9thqbaSLYNU31jCZ4FCdUoYbraAUW3=+<a href="mailto:o4wM%2BCSBJqA@mail.gmail.com" target="_blank">o4wM+CSBJqA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<div><div class="h5"><br>
<br>
Hi All,<br>
<br>
I'm getting an error when I run mne.make_forward_solution, but only if I<br>
try to save the result.<br>
<br>
That is, if I set fname=None then the whole thing runs fine, but if I set<br>
fname=<filename>, it fails in the call to write_forward_solution with the<br>
error:<br>
Head<-->sensor transform not found<br>
<br>
Seems like write_forward_solution is expecting values in info under<br>
dev_head_t or ctf_head_t, which never got set.<br>
<br>
I think it may be related to the fact that I'm loading (just EEG) data from<br>
a brainvision file using mne.io.read_raw_brainvision.<br>
<br>
I've been struggling to figure out how to include the digitizer information<br>
in the preprocessed data. My digitizer info is in a .fif file that<br>
otherwise doesn't contain any measurement data (I can't even figure out how<br>
to load it using the python MNE). So far the only thing I've done with that<br>
file is to use it to update the channel locations with a call to the C<br>
implementation:<br>
call(['mne_check_eeg_locations',<br>
'--file', fname,<br>
'--dig', op.join(subjects_dir,subject,subject + '.fif'),<br>
'--fix'])<br>
<br>
I'm new to all of this (including python) so any help would be much<br>
appreciated! I've attached the code (apologies for the mess).<br>
<br>
Thanks,<br>
Emily<br></div></div>
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------------------------------<br>
<br>
Message: 2<br>
Date: Tue, 17 Nov 2015 22:13:03 -0500 (EST)<br>
From: "Hari Bharadwaj" <<a href="mailto:hari@nmr.mgh.harvard.edu" target="_blank">hari@nmr.mgh.harvard.edu</a>><br>
Subject: Re: [Mne_analysis] Error running make_forward_solution:<span class=""><br>
Head<-->sensor transform not found<br></span>
To: "Discussion and support forum for the users of MNE Software"<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>><br>
Cc: <a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a><br>
Message-ID:<br>
<<a href="mailto:51230.24.34.210.250.1447816383.squirrel@mail.nmr.mgh.harvard.edu" target="_blank">51230.24.34.210.250.1447816383.squirrel@mail.nmr.mgh.harvard.edu</a>><br>
Content-Type: text/plain;charset=iso-8859-1<br>
<br>
Hi Emily,<br>
Perhaps you could try converting the digitization data to one of the<br>
formats (e.g., .hpts) accepted by mne.channels.read_montage(.) using<br>
the C-version of mne_convert_dig_data (if they are already not<br>
available in one of those formats). Once you do that and read it into<br>
python as a Montage object using mne.channels.read_montage(.), you<br>
could supply it as to the montage argument in<br>
mne.io.read_raw_brainvision(.).<br>
<br>
Also, the digitization data should contain cardinal points (like nasion,<br>
LPA, RAP) for the head along with the EEG sensor locations.. That way,<br>
"head coordinated" and "sensor coordinates" can be matched in the Montage.<br>
<br>
HTH,<br>
Hari<div><div class="h5"><br>
<br>
<br>
On Tue, November 17, 2015 7:07 pm, Emily Stephen wrote:<br>
> Hi All,<br>
><br>
> I'm getting an error when I run mne.make_forward_solution, but only if I<br>
> try to save the result.<br>
><br>
> That is, if I set fname=None then the whole thing runs fine, but if I set<br>
> fname=<filename>, it fails in the call to write_forward_solution with the<br>
> error:<br>
> Head<-->sensor transform not found<br>
><br>
> Seems like write_forward_solution is expecting values in info under<br>
> dev_head_t or ctf_head_t, which never got set.<br>
><br>
> I think it may be related to the fact that I'm loading (just EEG) data<br>
> from<br>
> a brainvision file using mne.io.read_raw_brainvision.<br>
><br>
> I've been struggling to figure out how to include the digitizer<br>
> information<br>
> in the preprocessed data. My digitizer info is in a .fif file that<br>
> otherwise doesn't contain any measurement data (I can't even figure out<br>
> how<br>
> to load it using the python MNE). So far the only thing I've done with<br>
> that<br>
> file is to use it to update the channel locations with a call to the C<br>
> implementation:<br>
> call(['mne_check_eeg_locations',<br>
> '--file', fname,<br>
> '--dig', op.join(subjects_dir,subject,subject + '.fif'),<br>
> '--fix'])<br>
><br>
> I'm new to all of this (including python) so any help would be much<br>
> appreciated! I've attached the code (apologies for the mess).<br>
><br>
> Thanks,<br>
> Emily<br></div></div>
> _______________________________________________<br>
> Mne_analysis mailing list<br>
> <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
> <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
<br>
<br>
--<br>
Hari Bharadwaj<br>
Research Fellow<br>
Martinos Center for Biomedical Imaging,<br>
Massachusetts General Hospital<br>
149 Thirteenth Street,<br>
Charlestown, MA 02129<br>
<br>
<a href="mailto:hari@nmr.mgh.harvard.edu" target="_blank">hari@nmr.mgh.harvard.edu</a><br>
Ph: <a href="tel:734-883-5954" value="+17348835954" target="_blank">734-883-5954</a><br>
<a href="http://www.haribharadwaj.com" rel="noreferrer" target="_blank">www.haribharadwaj.com</a><br>
<br>
<br>
------------------------------<br>
<br>
Message: 3<br>
Date: Wed, 18 Nov 2015 08:44:22 -0500<br>
From: Eric Larson <<a href="mailto:larson.eric.d@gmail.com" target="_blank">larson.eric.d@gmail.com</a>><br>
Subject: Re: [Mne_analysis] Error running make_forward_solution:<span class=""><br>
Head<-->sensor transform not found<br></span>
To: Discussion and support forum for the users of MNE Software<br>
<<a href="mailto:mne_analysis@nmr.mgh.harvard.edu" target="_blank">mne_analysis@nmr.mgh.harvard.edu</a>><br>
Message-ID:<br>
<CAGu2niVt3EnAv1566f=<a href="mailto:JjFWXVBof-yrC09f0M_%2BNTs60mKrPrg@mail.gmail.com" target="_blank">JjFWXVBof-yrC09f0M_+NTs60mKrPrg@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Can you simplify the script to use a minimal number of files and lines to<br>
reproduce the error (e.g., hopefully it doesn't depend on bad channels at<br>
all), and upload the necessary files and script somewhere? I guess that<br>
error could happen if you only have sensors in head coordinates to start<br>
with -- we can probably work around it.<br>
<br>
It shouldn't be too difficult to add that digitization information without<br>
having to resort to MNE-C tools. Feel free to open an mne-python issue<br>
about this stuff so we can hash out a solution, then we can report back to<br>
this thread.<br>
<br>
Eric<br>
<br>
<br>
On Tue, Nov 17, 2015 at 10:13 PM, Hari Bharadwaj <<a href="mailto:hari@nmr.mgh.harvard.edu" target="_blank">hari@nmr.mgh.harvard.edu</a>><br>
wrote:<br>
<br>
> Hi Emily,<br>
> Perhaps you could try converting the digitization data to one of the<br>
> formats (e.g., .hpts) accepted by mne.channels.read_montage(.) using<br>
> the C-version of mne_convert_dig_data (if they are already not<br>
> available in one of those formats). Once you do that and read it into<br>
> python as a Montage object using mne.channels.read_montage(.), you<br>
> could supply it as to the montage argument in<br>
> mne.io.read_raw_brainvision(.).<br>
><br>
> Also, the digitization data should contain cardinal points (like nasion,<br>
> LPA, RAP) for the head along with the EEG sensor locations.. That way,<br>
> "head coordinated" and "sensor coordinates" can be matched in the Montage.<br>
><br>
> HTH,<br>
> Hari<div><div class="h5"><br>
><br>
><br>
> On Tue, November 17, 2015 7:07 pm, Emily Stephen wrote:<br>
> > Hi All,<br>
> ><br>
> > I'm getting an error when I run mne.make_forward_solution, but only if I<br>
> > try to save the result.<br>
> ><br>
> > That is, if I set fname=None then the whole thing runs fine, but if I set<br>
> > fname=<filename>, it fails in the call to write_forward_solution with the<br>
> > error:<br>
> > Head<-->sensor transform not found<br>
> ><br>
> > Seems like write_forward_solution is expecting values in info under<br>
> > dev_head_t or ctf_head_t, which never got set.<br>
> ><br>
> > I think it may be related to the fact that I'm loading (just EEG) data<br>
> > from<br>
> > a brainvision file using mne.io.read_raw_brainvision.<br>
> ><br>
> > I've been struggling to figure out how to include the digitizer<br>
> > information<br>
> > in the preprocessed data. My digitizer info is in a .fif file that<br>
> > otherwise doesn't contain any measurement data (I can't even figure out<br>
> > how<br>
> > to load it using the python MNE). So far the only thing I've done with<br>
> > that<br>
> > file is to use it to update the channel locations with a call to the C<br>
> > implementation:<br>
> > call(['mne_check_eeg_locations',<br>
> > '--file', fname,<br>
> > '--dig', op.join(subjects_dir,subject,subject + '.fif'),<br>
> > '--fix'])<br>
> ><br>
> > I'm new to all of this (including python) so any help would be much<br>
> > appreciated! I've attached the code (apologies for the mess).<br>
> ><br>
> > Thanks,<br>
> > Emily<br></div></div>
> > _______________________________________________<br>
> > Mne_analysis mailing list<br>
> > <a href="mailto:Mne_analysis@nmr.mgh.harvard.edu" target="_blank">Mne_analysis@nmr.mgh.harvard.edu</a><br>
> > <a href="https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis" rel="noreferrer" target="_blank">https://mail.nmr.mgh.harvard.edu/mailman/listinfo/mne_analysis</a><br>
><br>
><br>
> --<br>
> Hari Bharadwaj<br>
> Research Fellow<br>
> Martinos Center for Biomedical Imaging,<br>
> Massachusetts General Hospital<br>
> 149 Thirteenth Street,<br>
> Charlestown, MA 02129<br>
><br>
> <a href="mailto:hari@nmr.mgh.harvard.edu" target="_blank">hari@nmr.mgh.harvard.edu</a><br>
> Ph: <a href="tel:734-883-5954" value="+17348835954" target="_blank">734-883-5954</a><br>
> <a href="http://www.haribharadwaj.com" rel="noreferrer" target="_blank">www.haribharadwaj.com</a><br>
> _______________________________________________<br>
> Mne_analysis mailing list<br>
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</blockquote></div><br></div></div>
</blockquote></div><br></div></div>