<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Looking at the spm-faces raw info:<div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">In [3]: </span><a href="http://raw.info" class="">raw.info</a>['dig']</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class="">Out[3]: </div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">[{'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 3,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 4.30736691e-09, 9.82968360e-02, 0.00000000e+00], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ -7.32455477e-02, -3.20142135e-09, 0.00000000e+00], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 7.07898811e-02, 2.96859071e-09, 0.00000000e+00], dtype=float32)}]</div><div class=""><br class=""></div><div class="">but in the GUI we are selecting fiducial points with </div><div class=""><br class=""></div><div class=""><pre style="background-color:#2b2b2b;color:#a9b7c6;font-family:'Menlo';font-size:12.0pt;" class="">d[<span style="color:#a5c261;" class="">'kind'</span>] == FIFF.FIFFV_POINT_CARDINAL</pre><div class="">and</div></div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">In [8]: </span>FIFF.FIFFV_POINT_CARDINAL</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class="">Out[8]: <span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class="">1</span></div></div><div class=""><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">In [12]: </span>FIFF.FIFFV_POINT_HPI</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class="">Out[12]: <span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class="">2</span></div></div><div class=""><span style="font-variant-ligatures: no-common-ligatures; color: #f5f5f5" class=""><br class=""></span></div><div class="">so, is there something wrong with the spm-faces file (Fiducials stored as HPI)? Or are fiducials sometimes identical with HPI and the GUI should use them as such?</div><div class=""><br class=""></div><div class="">The latter would actually cause a conflict with our KIT files, because HPI points and fiducials which are not identical have the same “ident”:</div><div class=""><br class=""></div><div class=""><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""><span style="font-variant-ligatures: no-common-ligatures; color: #5330e1" class="">In [16]: </span>[d for d in <a href="http://kraw.info" class="">kraw.info</a>['dig'] if d['kind'] < 3]</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(195, 55, 32); background-color: rgb(0, 0, 0);" class="">Out[16]: </div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class="">[{'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 0.00000000e+00, 1.07987508e-01, -1.38777878e-17], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ -7.57353827e-02, 1.04083409e-17, 1.38777878e-17], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 3,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 6.99156001e-02, 0.00000000e+00, 1.38777878e-17], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 0,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([-0.07321275, 0.0070182 , -0.00094954], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 1,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 0.06706881, 0.01023183, -0.00318275], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 0.00344993, 0.11684198, 0.02777481], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 3,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([-0.03729108, 0.1059907 , 0.03130391], dtype=float32)},</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> {'coord_frame': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'ident': 4,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'kind': 2,</div><div style="margin: 0px; font-size: 10px; line-height: normal; font-family: Monaco; color: rgb(245, 245, 245); background-color: rgb(0, 0, 0);" class=""> 'r': array([ 0.0470689 , 0.09996997, 0.03072358], dtype=float32)}]</div></div><div class=""><br class=""></div><div class="">Although a potential solution could use HPI only if no Cardinal points are present?</div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""></div><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On Oct 4, 2015, at 11:02 AM, Alexandre Gramfort <<a href="mailto:alexandre.gramfort@telecom-paristech.fr" class="">alexandre.gramfort@telecom-paristech.fr</a>> wrote:</div><br class="Apple-interchange-newline"><div class=""><div class="">hi Annalisa,<br class=""><br class=""><blockquote type="cite" class="">I have two different questions about the example plot_spm_faces_dataset.py.<br class=""><br class="">1) If I run the code and I try to plot the ICA components on time<br class=""><br class=""><blockquote type="cite" class=""><blockquote type="cite" class=""><blockquote type="cite" class=""> show_picks = numpy.abs(eog_scores).argsort()[::-1][:5]<br class=""> fig1=ica.plot_sources(raw, show_picks, exclude=eog_inds)<br class=""></blockquote></blockquote></blockquote><br class=""> I obtain the figure u find in attachment.<br class=""> My question is: why do I see the ref channels?<br class=""><br class=""> In the old mne-python version I had a different layout, as that<br class=""> shown in plot_ica_from_raw.py.<br class=""><br class=""> What's wrong?<br class=""></blockquote><br class="">we improved the layout. But indeed there is no point is showing the<br class="">meg reference channels.<br class=""><br class="">We'll fix it this week.<br class=""><br class=""><blockquote type="cite" class="">2) I tried to co-register using mne.gui.coregistration()<br class=""><br class=""> I load the spm sbj and the raw file<br class="">SPM_CTF_MEG_example_faces1_3D_raw.fif.<br class=""> Does this file contain only the fiducial points?<br class=""></blockquote><br class="">yes<br class=""><br class=""><blockquote type="cite" class=""> If yes, when I load the raw file I can't see the fiducials in the gui.<br class=""></blockquote><br class="">maybe Christian knows. Do you see them with mne_analyze?<br class=""><br class=""><blockquote type="cite" class=""> Where I'm making a mistake?<br class=""></blockquote><br class="">I don't think you do :)<br class=""><br class="">Best,<br class="">Alex<br class=""></div></div></blockquote></div><br class=""></div></div></body></html>