[Mne_analysis] Fwd: Maxfilter error: ill conditioned matrix

[Sophie Herbst]

        External Email - Use Caution        

Dear Eric,
thank you for the code snippet! I adapted it to my data and indeed, 3
participants (for whom I get the maxfilter error) come out of the recording
with a completely distorted head position for all or some runs (see pic). I
know I positioned them correctly and the HPI that I measure at the
beginning of a run was ok (3/4 coils fine).
So I am afraid, the dev_head_t is off.
Do you have any idea of how that could have happend? Is there anything I
could do to fix this?
I already tried hpifit from the elekta tools, but re-ordering the coils
does not solve it.
Thank you,
Sophie
[image: Folie1.png]


Sophie Herbst <ksherbst at googlemail.com> schrieb am Mo., 23. Apr. 2018 um
09:35 Uhr:

> ---------- Forwarded message ---------
> From: Eric Larson <larson.eric.d at gmail.com>
> Date: Fr., 20. Apr. 2018 um 18:30 Uhr
> Subject: Re: [Mne_analysis] Maxfilter error: ill conditioned matrix
> To: Discussion and support forum for the users of MNE Software <
> mne_analysis at nmr.mgh.harvard.edu>
>
>
>         External Email - Use Caution
>
> destination =
>> <Transform  |  MEG device->head>
>> [[ 0.71960711  0.63715118 -0.27605024 -0.07788484]
>>  [-0.67182261  0.73935592 -0.04479922 -0.01268383]
>>  [ 0.17555553  0.21769466  0.96009851  0.06360817]
>>  [ 0.          0.          0.          1.        ]]
>>
>
> This appears to have a large rotation and translation. To confirm, we can
> take a look at what this transformation would be like for the "sample"
> subject:
>
> import mne
> data_path = mne.datasets.sample.data_path()
> raw = mne.io.read_raw_fif(data_path + '/MEG/sample/sample_audvis_raw.fif')raw.info['dev_head_t']['trans'] = np.array(
>     [[ 0.71960711,  0.63715118, -0.27605024, -0.07788484],
>      [-0.67182261,  0.73935592, -0.04479922, -0.01268383],
>      [ 0.17555553,  0.21769466,  0.96009851,  0.06360817],
>      [ 0.,          0.,          0.,          1.        ]])
> trans = mne.read_trans(data_path + '/MEG/sample/sample_audvis_raw-trans.fif')
> mne.viz.plot_alignment(raw.info, trans=trans, subject='sample',
>                        subjects_dir=data_path + '/subjects',
>                        coord_frame='meg', dig=True)
>
> ​
> This view from the front of the MEG helmet looks like:
>
> [image: snapshot.png]
>
> I recommend adapting this script to use your own data, as it will show the
> correct digitization (and correct head if you have an MRI, if not, omit the
> subject* and trans parameters, and set surfaces=[] in the plot_alignment
> call). Was this roughly the orientation and position of the subject during
> acquisition? If not, your dev_head_t is probably incorrect.
>
> The actual origin used by Maxfilter will also depend on what you pass as
> the "origin" parameter. But in any case, it appears that it will be quite
> far from the device origin, and quite close to one side of the helmet (or
> maybe outside it). This is probably causing the conditioning problems.
> Assuming the dev_head_t is indeed correct, you should inspect the resulting
> transform to see if it has amplified some of the noise, which (I think) is
> a potential risk when the condition number gets too large.
>
> Eric
>
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