<div dir="ltr"><div dir="ltr">Hi Jan-Mathijis<div><br></div><div>Thanks for the suggestion. Now, I load the freesurfer T1.mgz, I change the transformation matrix obtained from the command mri_info --vox2ras-tkr and then I align the T1.mgz and with the obtained transformation matrix I transform the surface. If I create a headmodel from the T1.mgz the surface is perfectly aligned, however, if I use a headmodel from the original mri it is slightly not aligned. For some reason, the T1.mgz headshape alignment is less precise (as measured by the average distance of the polhemus and the scalp points). Do you know why is that? Is it possible to align the subject-space aligned T1.mgz with the subject-space aligned mri?</div><div><br></div><div>For the posterity that is the code I used:</div><div><br></div><div>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(178,69,243)"><span class="gmail-s1" style="color:rgb(0,0,0)">system(</span>'mri_info --vox2ras-tkr /path2/T1.mgz > /path2/t1-vox2ras-tkr.xfm'<span class="gmail-s1" style="color:rgb(0,0,0)">)</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">t1 = ft_read_mri(<span class="gmail-s2" style="color:rgb(178,69,243)">'/path2/T1.mgz'</span>);</p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(178,69,243)"><span class="gmail-s1" style="color:rgb(0,0,0)">t1.transform = load(</span>'/path2/t1-vox2ras-tkr.xfm'<span class="gmail-s1" style="color:rgb(0,0,0)">);</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg=[];</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.method<span class="gmail-Apple-converted-space"> </span>=<span class="gmail-Apple-converted-space"> </span><span class="gmail-s2" style="color:rgb(178,69,243)">'interactive'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.coordsys<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'ctf'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.viewmode<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'ortho'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">mri_aligned1<span class="gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg,t1);</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><span class="gmail-Apple-converted-space"> </span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg=[];</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.method<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'headshape'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.headshape.headshape = polhemus;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.coordsys<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'ctf'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.headshape.interactive<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'no'</span>;</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">cfg.headshape.icp<span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s2" style="color:rgb(178,69,243)">'yes'</span>;</p>
<p class="gmail-p4" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(37,153,45)"><span class="gmail-s1" style="color:rgb(0,0,0)">cfg.checksize = 1e10 ; </span>% don't remove scalp segmentation from output</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">mri_aligned2<span class="gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg,mri_aligned1 );</p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px"><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;color:rgb(178,69,243)"><span class="gmail-s1" style="color:rgb(0,0,0)">sourcespace = ft_read_headshape({</span>'/path2/surf/lh.white'<span class="gmail-s1" style="color:rgb(0,0,0)">,</span>'/path2/surf/rh.white'<span class="gmail-s1" style="color:rgb(0,0,0)">});</span></p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">sourcespace = ft_convert_units(sourcespace, <span class="gmail-s2" style="color:rgb(178,69,243)">'mm'</span>);</p>
<p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">sourcespace = ft_transform_geometry(mri_aligned2.transform/t1.transform, sourcespace);</p><p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier"><br></p><p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">Thanks for your help,</p><p class="gmail-p3" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">Dorothy</p></div></div></div><br><div class="gmail_quote"><div dir="ltr">On Fri, Sep 21, 2018 at 1:35 AM Schoffelen, J.M. (Jan Mathijs) <<a href="mailto:jan.schoffelen@donders.ru.nl">jan.schoffelen@donders.ru.nl</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div style="word-wrap:break-word">
Hi Dorothy,
<div><br>
</div>
<div>The best way to do this is indeed to follow the tutorial. If you don’t want to rerun the freesurfer pipeline things only get complicated.</div>
<div>The code you pasted is not correct, because of the reslicing step in between. Creating the ’T’ matrix as a combination of two vox2somethingelse transformation matrices is only allowed if the voxel spaces that correspond to each of the transformations
is identical. </div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div>PS: If you insist on trying it, the best way to go about this would be to use the T1w.mgz anatomical image from the freesurfer mri folder for the headmodel creation. Before the headmodel creation, you probably would want to coregister this image
to the coordinate system of your EEG/MEG sensors.</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div style="word-wrap:break-word">
<div style="word-wrap:break-word">
<div style="word-wrap:break-word">
J.M.Schoffelen, MD PhD<br>
Senior Researcher, VIDI-fellow - PI, language in interaction<br>
Telephone: +31-24-3614793</div>
<div style="word-wrap:break-word">
Physical location: room 00.028</div>
<div style="word-wrap:break-word">
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br>
<br>
<br>
</div>
</div>
</div>
</div>
</div>
<div><br>
</div>
<div><br>
<div>
<blockquote type="cite">
<div>On 19 Sep 2018, at 22:41, Dorothy Sincasto <<a href="mailto:dsincasto@gmail.com" target="_blank">dsincasto@gmail.com</a>> wrote:</div>
<br class="m_-6483841335407044986Apple-interchange-newline">
<div>
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">
<div dir="ltr">Dear fieldtrippers
<div><br>
</div>
<div>I would like to align the headmodel of a subject with the freesurfer surface. It seems that this is a bit different than the fieldtrip mne tutorial, as we already have the freesurfer surfaces (so we did not align the mri, save them and run freesurfer).</div>
<div><br>
</div>
<div>To try to convert the freesurface surface coordinates to the subjects MEG coordinates I do:</div>
<div>
<p class="m_-6483841335407044986gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span><br class="m_-6483841335407044986webkit-block-placeholder">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg = [];</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.method = <span class="m_-6483841335407044986gmail-s1" style="color:rgb(178,69,243)">'interactive'</span>;</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.coordsys = <span class="m_-6483841335407044986gmail-s1" style="color:rgb(178,69,243)">'spm'</span>;</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
mri_spm<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg, mri);</div>
<p class="m_-6483841335407044986gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span><br class="m_-6483841335407044986webkit-block-placeholder">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= [];</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.resolution = 1;</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.dim<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= [256 256 256];</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
mri_spm_rs <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= ft_volumereslice(cfg, mri);</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
transform_vox2spm = mri_spm_rs.transform;</div>
<p class="m_-6483841335407044986gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span><br class="m_-6483841335407044986webkit-block-placeholder">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= [];</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.method <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= <span class="m_-6483841335407044986gmail-s1" style="color:rgb(178,69,243)">
'interactive'</span>;</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
cfg.coordsys = <span class="m_-6483841335407044986gmail-s1" style="color:rgb(178,69,243)">'ctf'</span>;</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
mri_ctf_rs <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg, mri_spm_rs);</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
transform_vox2ctf = mri_ctf_rs.transform;</div>
<p class="m_-6483841335407044986gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier;min-height:12px">
<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span><br class="m_-6483841335407044986webkit-block-placeholder">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
T = transform_vox2ctf/transform_vox2spm;</div>
<p class="m_-6483841335407044986gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
</p>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
sourcespace = ft_read_headshape({my_surface}</div>
</div>
<div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:10px;line-height:normal;font-family:Courier">
sourcespace = ft_transform_geometry(T, sourcespace);</div>
</div>
<div><br>
</div>
<div>However, although the surface and headmodel is quite aligned, the surface is a bit lower and posterior than the headmodel, as can be seen in this screenshot: <a href="https://ibb.co/eEVV2K" target="_blank">https://ibb.co/eEVV2K</a></div>
<div><br>
</div>
<div>We also tried the transformation matrices from freesurfer outputed with the command mri_info surface.surf</div>
<div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures">voxel to ras transform:</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-1.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>131.6938</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>1.0000<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>-111.6126</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>-1.0000<span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>157.1196</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>1.0000</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures">voxel-to-ras determinant -1</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br>
</div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures">ras to voxel transform:</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-1.0000<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>-0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>131.6938</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>-0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-1.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>157.1196</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>1.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>111.6126</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<span class="m_-6483841335407044986gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>-0.0000<span class="m_-6483841335407044986gmail-Apple-converted-space">
</span>-0.0000 <span class="m_-6483841335407044986gmail-Apple-converted-space"> </span>1.0000</span></div>
<div style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">
<br>
</div>
</div>
<div>But the results are worse. I am a bit desperate in finding a way to align the surface without having to rerun freesurface on all the subjects. </div>
<div><br>
</div>
<div>Is there a method to properly align the freesurfer surface to the aligned headmodel?</div>
<div><br>
</div>
<div>Thank you</div>
<div>Dorothy</div>
</div>
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</blockquote>
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</div>
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</blockquote></div>