<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:"Calibri Light";
panose-1:2 15 3 2 2 2 4 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Times;
panose-1:2 2 6 3 5 4 5 2 3 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
mso-fareast-language:EN-US;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
p
{mso-style-priority:99;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
p.msonormal0, li.msonormal0, div.msonormal0
{mso-style-name:msonormal;
mso-margin-top-alt:auto;
margin-right:0cm;
mso-margin-bottom-alt:auto;
margin-left:0cm;
font-size:12.0pt;
font-family:"Times New Roman",serif;}
span.E-postmall18
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.pl-k
{mso-style-name:pl-k;}
span.pl-s
{mso-style-name:pl-s;}
span.pl-pds
{mso-style-name:pl-pds;}
span.pl-v
{mso-style-name:pl-v;}
span.pl-c1
{mso-style-name:pl-c1;}
p.p1, li.p1, div.p1
{mso-style-name:p1;
margin:0cm;
margin-bottom:.0001pt;
line-height:10.5pt;
font-size:9.0pt;
font-family:"Times",serif;
color:black;}
p.p2, li.p2, div.p2
{mso-style-name:p2;
margin:0cm;
margin-bottom:.0001pt;
line-height:10.5pt;
font-size:9.0pt;
font-family:"Times",serif;
color:black;}
span.s2
{mso-style-name:s2;
color:#0000EE;
text-decoration:underline;}
span.s1
{mso-style-name:s1;}
span.apple-converted-space
{mso-style-name:apple-converted-space;}
span.E-postmall30
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:#1F497D;}
span.E-postmall31
{mso-style-type:personal-compose;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 70.85pt 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body lang="EN-GB" link="#0563C1" vlink="#954F72"><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 class="WordSection1">
<p class="MsoNormal"><span style="color:#1F497D">Solved my problem: <o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri Light",sans-serif"> morph = mne.compute_source_morph(stc_subject, subject, 'fsaverage', subjects_dir=subjects_dir,
<b>spacing=4</b>) # New in MNE 0.17<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri Light",sans-serif"> stc_fsaverage = morph.apply(stc_subject)<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Best regards<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D">Mikkel<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<p class="MsoNormal"><b><span lang="SV" style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">Mikkel C. Vinding</span></b><span lang="SV" style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB"> | Ph.D. | Post doc<br>
NatMEG - </span><span lang="EN-US" style="font-size:10.0pt;color:#1F497D;background:white;mso-fareast-language:EN-GB">The National Research Facility for Magnetoencephalography
</span><span lang="SV" style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB"><br>
Department of Clinical Neuroscience | Karolinska Institutet<br>
171 77 Stockholm | Nobels väg 9, office D313<br>
</span><span lang="EN-US" style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB">Phone: +46 8 524 833 33
<br>
Email: </span><span lang="SV" style="font-size:10.0pt;color:#1F497D;mso-fareast-language:EN-GB"><a href="mailto:mikkel@vinding@ki.se" target="_blank"><span style="color:#1F497D">mikkel.</span></a><a href="mailto:mikkel.vinding@ki.se"><span style="color:#1F497D">vinding@ki.se
</span></a>| <a href="http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130">
<span style="color:#1F497D">ki.se</span></a><br>
______________________________________<br>
Karolinska Institutet – a medical university<o:p></o:p></span></p>
</div>
<p class="MsoNormal"><span style="color:#1F497D"><o:p> </o:p></span></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span lang="SV" style="mso-fareast-language:EN-GB">Från:</span></b><span lang="SV" style="mso-fareast-language:EN-GB"> mne_analysis-bounces@nmr.mgh.harvard.edu [mailto:mne_analysis-bounces@nmr.mgh.harvard.edu]
<b>För </b>Mikkel Vinding<br>
<b>Skickat:</b> den 4 december 2018 16:06<br>
<b>Till:</b> mne_analysis@nmr.mgh.harvard.edu<br>
<b>Ämne:</b> [Mne_analysis] morph.apply and source space size<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p><b><span style="color:white;background:red"> External Email - Use Caution </span></b><o:p></o:p></p>
<p class="MsoNormal">Dear MNE list<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can anyone help me how to keep the resolution of the source space when morphing source estimates from subject MRI space to fs_average. I use the new morphing function in MNE-Python 0.17:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span style="font-family:"Calibri Light",sans-serif"> morph = mne.compute_source_morph(stc_subject, subject, 'fsaverage', subjects_dir=subjects_dir) # New in MNE 0.17<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-family:"Calibri Light",sans-serif"> stc_fsaverage = morph.apply(stc_subject)<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">When the morphing is comple, it now contain all verticies from fs_average:<o:p></o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-family:"Calibri Light",sans-serif">stc_subject: <SourceEstimate | 5124 vertices, subject : 0403, tmin : 0.0 (ms), tmax : 0.0 (ms), tstep : 1000.0 (ms), data shape : (5124, 1)<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-family:"Calibri Light",sans-serif">stc_fsaverage: <SourceEstimate | 20484 vertices, subject : fsaverage, tmin : 0.0 (ms), tmax : 0.0 (ms), tstep : 1000.0 (ms), data shape : (20484, 1)><o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal">Is there a way to keep the original number of vertices in the morphed source maps?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">In the previous version of MNE-Python morphing had a “grade” argument:<o:p></o:p></p>
<p class="MsoNormal" style="text-indent:36.0pt"><span style="font-family:"Calibri Light",sans-serif">stc_fsaverage
<span class="pl-k">=</span> stc_subject.morph(<span class="pl-pds">'</span><span class="pl-s">fsaverage</span><span class="pl-pds">'</span>,
<span class="pl-v">subjects_dir</span><span class="pl-k">=</span>subjects_dir, <span class="pl-v">
grade</span><span class="pl-k">=</span><span class="pl-c1">4</span>)<o:p></o:p></span></p>
<p class="MsoNormal" style="text-indent:36.0pt"><o:p> </o:p></p>
<p class="MsoNormal">There is the argument “mri_resolution” in the morph.apply, but it does not seem to alter the scaling. Or maybe I am not giving it the correct argument: it is not 4 nor 5124?<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thank you in advance<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Best regards<o:p></o:p></p>
<p class="MsoNormal">Mikkel<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span lang="SV" style="font-size:10.0pt;mso-fareast-language:EN-GB">Mikkel C. Vinding</span></b><span lang="SV" style="font-size:10.0pt;mso-fareast-language:EN-GB"> | Ph.D. | Post doc<br>
NatMEG - </span><span lang="EN-US" style="font-size:10.0pt;background:white;mso-fareast-language:EN-GB">The National Research Facility for Magnetoencephalography
</span><span lang="SV" style="font-size:10.0pt;mso-fareast-language:EN-GB"><br>
Department of Clinical Neuroscience | Karolinska Institutet<br>
171 77 Stockholm | Nobels väg 9, office D313<br>
</span><span lang="EN-US" style="font-size:10.0pt;mso-fareast-language:EN-GB">Phone: +46 8 524 833 33
<br>
Email: </span><span lang="SV" style="font-size:10.0pt;mso-fareast-language:EN-GB"><a href="mailto:mikkel@vinding@ki.se" target="_blank"><span style="color:windowtext">mikkel.</span></a><a href="mailto:mikkel.vinding@ki.se"><span style="color:windowtext">vinding@ki.se
</span></a>| <a href="http://ki.se/ki/jsp/polopoly.jsp;jsessionid=aMdk8ad4iRL6OYOdFn?l=en&d=130">
<span style="color:windowtext">ki.se</span></a><br>
______________________________________<br>
Karolinska Institutet – a medical university<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="p1"><o:p> </o:p></p>
<p class="p1"><o:p> </o:p></p>
<p class="p2"><span class="s1"><i>När du skickar e-post till Karolinska Institutet (KI) innebär detta att KI kommer att behandla dina personuppgifter.
</i><a href="https://ki.se/medarbetare/integritetsskyddspolicy"><span class="s2">Här finns information om hur KI behandlar personuppgifter</span></a>.</span><span class="apple-converted-space"> </span><o:p></o:p></p>
<p class="p1"><o:p> </o:p></p>
<p class="p2"><span class="s1"><i>Sending email to Karolinska Institutet (KI) will result in KI processing your personal data.</i>
<a href="https://ki.se/en/staff/data-protection-policy"><span class="s2">You can read more about KI’s processing of personal data here</span></a>.</span><span class="apple-converted-space"> </span><o:p></o:p></p>
</div>
</body>
</html>