<p><span style="padding: 3px 10px; border-radius: 5px; color: #ffffff; font-weight: bold; display: inline-block; background-color: #ff0000;"> External Email - Use Caution </span></p><p></p><div dir="ltr"><div class="gmail_extra"><div class="gmail_quote"><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><span style="color:rgb(33,33,33)">destination = </span></div><div><span style="font-family:Tahoma;font-size:13.3333px"><Transform | MEG device->head></span></div><span style="font-family:Tahoma;font-size:13.3333px">[[ 0.71960711 0.63715118 -0.27605024 -0.07788484]</span><br style="font-family:Tahoma;font-size:13.3333px"><span style="font-family:Tahoma;font-size:13.3333px"> [-0.67182261 0.73935592 -0.04479922 -0.01268383]</span><br style="font-family:Tahoma;font-size:13.3333px"><span style="font-family:Tahoma;font-size:13.3333px"> [ 0.17555553 0.21769466 0.96009851 0.06360817]</span><br style="font-family:Tahoma;font-size:13.3333px"><span style="font-family:Tahoma;font-size:13.3333px"> [ 0. 0. 0. 1. ]]</span></div></blockquote><div><br></div><div>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:</div><div></div><div class="gmail-markdown-here-wrapper"><pre style="font-family:Consolas,Inconsolata,Courier,monospace;font-size:1em;line-height:1.2em;margin:1.2em 0px"><code style="font-size:0.85em;font-family:Consolas,Inconsolata,Courier,monospace;margin:0px 0.15em;background-color:rgb(248,248,248);white-space:pre;overflow:auto;border-radius:3px;border:1px solid rgb(204,204,204);padding:0.5em 0.7em;display:block">import mne
data_path = mne.datasets.sample.data_path()
raw = mne.io.read_raw_fif(data_path + '/MEG/sample/sample_audvis_raw.fif')
<a href="http://raw.info">raw.info</a>['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(<a href="http://raw.info">raw.info</a>, trans=trans, subject='sample',
subjects_dir=data_path + '/subjects',
coord_frame='meg', dig=True)
</code></pre><div title="MDH:PGRpdj5gYGA8L2Rpdj48ZGl2Pgo8cCBzdHlsZT0ibWFyZ2luOiAwcHg7IHdoaXRlLXNwYWNlOiBw
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ICAgICAgICAgIDAuLCAgICAgICAgICAxLiAgICAgICAgXV0pPC9wPgo8cCBzdHlsZT0ibWFyZ2lu
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cCBzdHlsZT0ibWFyZ2luOiAwcHg7IHdoaXRlLXNwYWNlOiBwcmUtd3JhcDsiPm1uZS52aXoucGxv
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PHAgc3R5bGU9Im1hcmdpbjogMHB4OyB3aGl0ZS1zcGFjZTogcHJlLXdyYXA7Ij4gICAgICAgICAg
ICAgICAgICAgICAgIHN1YmplY3RzX2Rpcj1kYXRhX3BhdGggKyAnL3N1YmplY3RzJyw8L3A+Cjxw
IHN0eWxlPSJtYXJnaW46IDBweDsgd2hpdGUtc3BhY2U6IHByZS13cmFwOyI+ICAgICAgICAgICAg
ICAgICAgICAgICBjb29yZF9mcmFtZT0nbWVnJyk8L3A+PC9kaXY+PGRpdj5gYGA8L2Rpdj48ZGl2
PjwvZGl2Pg==" style="height:0px;width:0px;max-height:0px;max-width:0px;overflow:hidden;font-size:0em;padding:0px;margin:0px"></div></div><div>This view from the front of the MEG helmet looks like:<br></div><div><br></div><div><img src="cid:ii_jg861o781_162e3dfdf14f97c6" style="margin-right: 0px;" width="224" height="210"><br><br></div><div>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.<br></div><div><br></div><div>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.</div><div><br></div><div>Eric</div><div><br></div></div></div></div>