<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="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;min-height:12px"><span class="gmail-Apple-converted-space"> </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">cfg = [];</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">cfg.method = <span class="gmail-s1" style="color:rgb(178,69,243)">'interactive'</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">cfg.coordsys = <span class="gmail-s1" style="color:rgb(178,69,243)">'spm'</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">mri_spm<span class="gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg, mri);</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;min-height:12px"><span class="gmail-Apple-converted-space"> </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">cfg<span class="gmail-Apple-converted-space"> </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">cfg.resolution = 1;</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">cfg.dim<span class="gmail-Apple-converted-space"> </span>= [256 256 256];</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">mri_spm_rs <span class="gmail-Apple-converted-space"> </span>= ft_volumereslice(cfg, mri);</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">transform_vox2spm = mri_spm_rs.transform;</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;min-height:12px"><span class="gmail-Apple-converted-space"> </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">cfg<span class="gmail-Apple-converted-space"> </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">cfg.method <span class="gmail-Apple-converted-space"> </span>= <span class="gmail-s1" style="color:rgb(178,69,243)">'interactive'</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">cfg.coordsys = <span class="gmail-s1" style="color:rgb(178,69,243)">'ctf'</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">mri_ctf_rs <span class="gmail-Apple-converted-space"> </span>= ft_volumerealign(cfg, mri_spm_rs);</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">transform_vox2ctf = mri_ctf_rs.transform;</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;min-height:12px"><span class="gmail-Apple-converted-space"> </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">T = transform_vox2ctf/transform_vox2spm;</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">
</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">sourcespace = ft_read_headshape({my_surface}</p></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">sourcespace = ft_transform_geometry(T, sourcespace);</p></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">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>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">voxel to ras transform:</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>-1.0000 <span class="gmail-Apple-converted-space"> </span>0.0000<span class="gmail-Apple-converted-space"> </span>-0.0000 <span class="gmail-Apple-converted-space"> </span>131.6938</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>1.0000<span class="gmail-Apple-converted-space"> </span>-111.6126</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>-0.0000<span class="gmail-Apple-converted-space"> </span>-1.0000<span class="gmail-Apple-converted-space"> </span>-0.0000 <span class="gmail-Apple-converted-space"> </span>157.1196</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>1.0000</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">voxel-to-ras determinant -1</span></p>
<p class="gmail-p2" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0);min-height:13px"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"></span><br></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures">ras to voxel transform:</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>-1.0000<span class="gmail-Apple-converted-space"> </span>-0.0000<span class="gmail-Apple-converted-space"> </span>-0.0000 <span class="gmail-Apple-converted-space"> </span>131.6938</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>0.0000<span class="gmail-Apple-converted-space"> </span>-0.0000<span class="gmail-Apple-converted-space"> </span>-1.0000 <span class="gmail-Apple-converted-space"> </span>157.1196</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>1.0000 <span class="gmail-Apple-converted-space"> </span>0.0000 <span class="gmail-Apple-converted-space"> </span>111.6126</span></p>
<p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><span class="gmail-s1" style="font-variant-ligatures:no-common-ligatures"><span class="gmail-Apple-converted-space"> </span>-0.0000<span class="gmail-Apple-converted-space"> </span>-0.0000<span class="gmail-Apple-converted-space"> </span>-0.0000 <span class="gmail-Apple-converted-space"> </span>1.0000</span></p><p class="gmail-p1" style="margin:0px;font-variant-numeric:normal;font-variant-east-asian:normal;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;color:rgb(0,0,0)"><br></p></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></div></div></div></div></div>