<div dir="ltr">Hi <span style="font-size:13px">Jan-Mathijs</span><div>Thanks for getting back to me so quickly. I originally used Ft_sensoralign, but I got the error messages one of which said </div><div>'FT_SENSORREALIGN is deprecated, please use FT_ELECTRODEREALIGN instead' so thats why I used electrode realign instead, even though it's MEG data. </div><div><br></div><div>I've been following this page to do the realignment. </div><div><br></div><div><a href="http://www.fieldtriptoolbox.org/getting_started/yokogawa?s[]=yokogawa">http://www.fieldtriptoolbox.org/getting_started/yokogawa?s[]=yokogawa</a><br></div><div><br></div><div>if I use sensorrealign how should I deal with these error messages? </div><div><br></div><div><div style="font-size:13px">Undefined function or variable 'lab'.</div><div style="font-size:13px"><br></div><div style="font-size:13px">Error in channelposition (line 314)</div><div style="font-size:13px">n = size(lab,2);</div><div style="font-size:13px"><br></div><div style="font-size:13px">Error in ft_datatype_sens (line 328)</div><div style="font-size:13px"> [chanpos, chanori, lab] = channelposition(sens);</div><div style="font-size:13px"><br></div><div style="font-size:13px">Error in ft_sensorrealign (line 212)</div><div style="font-size:13px">elec_original = ft_datatype_sens(elec_<wbr>original); % ensure up-to-date sensor description (Oct 2011)</div></div><div style="font-size:13px"><br></div><div style="font-size:13px"><br></div><div style="font-size:13px">is there another way to realign my anatomical with my MEG sensors without using ft_sensorrealign?</div><div style="font-size:13px"><br></div><div style="font-size:13px">Thanks,</div><div style="font-size:13px">Ainsley </div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Mar 8, 2017 at 11:26 AM, Schoffelen, J.M. (Jan Mathijs) <span dir="ltr"><<a href="mailto:jan.schoffelen@donders.ru.nl" target="_blank">jan.schoffelen@donders.ru.nl</a>></span> wrote:<br><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 Ainsley,
<div><br>
</div>
<div>Why would you want to use sensorrealign/electroderealign since you have MEG-data? The former functions may be needed for EEG electrodes, not for MEG sensors.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div style="word-wrap:break-word">
J.M.Schoffelen, MD PhD<br>
Senior Researcher, VIDI-fellow - PI, language in interaction<br>
Telephone: <a href="tel:+31%2024%20361%204793" value="+31243614793" target="_blank">+31-24-3614793</a></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>
</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite"><div><div class="h5">
<div>On 08 Mar 2017, at 07:52, Ainsley Temudo <<a href="mailto:ainsley.temudo@nyu.edu" target="_blank">ainsley.temudo@nyu.edu</a>> wrote:</div>
<br class="m_-4831077437308618983Apple-interchange-newline">
</div></div><div><div><div class="h5">
<div dir="ltr">
<div>Hi FieldTrip Experts,</div>
<div><br>
</div>
<div>I am trying to perform source reconstruction, and I am having trouble with coregistering my anatomical with the sensors. The MEG system we're using is Yokogawa and the anatomical is a NIFTI file. I get some errors when using ft_sensorrealign
and ft_electroderealign. I will go through the steps I took before getting to this stage, as maybe I have done something wrong. </div>
<div><br>
</div>
<div>first I read in my MRI and determine the coordinate system which is LPS.</div>
<div><br>
</div>
<div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
mriunknown = ft_read_mri(<span style="color:rgb(178,69,243)">'WMCP1011+22+<wbr>t1mprage.nii'</span>);</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
mri = ft_determine_coordsys(<wbr>mriunknown, <span style="color:rgb(178,69,243)">
'interactive'</span>,<span style="color:rgb(178,69,243)">'yes'</span>)</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<br>
</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<span style="font-family:arial,sans-serif;font-size:small"> next I realign to the CTF coordinate system by marking the NAS LPA, RPA </span><br>
</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<span style="font-family:arial,sans-serif;font-size:small"><br>
</span></div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg = [];</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.method = <span style="color:rgb(178,69,243)">'interactive'</span>;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.coordsys = <span style="color:rgb(178,69,243)">'ctf'</span>;</div>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
</p>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
mri_ctf = ft_volumerealign(cfg, mir);</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<br>
</div>
<div style="margin:0px;line-height:normal">I read in the sensor information and added in the coordinates for the marker positions. we have five marker positions, the three I picked were the left and right ear markers and the middle forehead marker.
</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<span><br>
</span></div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<span>grad=ft_read_sens(</span><span style="color:rgb(178,69,243)">'<wbr>srcLocTest01_FT_01.con'</span><span>);</span><br>
</div>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier;min-height:12px">
<br class="m_-4831077437308618983webkit-block-placeholder">
</p>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier;min-height:12px">
<br class="m_-4831077437308618983webkit-block-placeholder">
</p>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
grad.fid.pnt(1,:) = [96.07 3.11 -5.32]./10;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
grad.fid.pnt(2,:) = [11.13 75.50 -78.23]./10;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
grad.fid.pnt(3,:) = [8.50 -75.09 -64.60]./10;</div>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier;min-height:12px">
<br class="m_-4831077437308618983webkit-block-placeholder">
</p>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
grad.fid.label = {<span style="color:rgb(178,69,243)">'NAS'</span> <span style="color:rgb(178,69,243)">'LPA'</span> <span style="color:rgb(178,69,243)">'RPA'</span>};</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<br>
</div>
<div style="margin:0px;line-height:normal;min-height:12px">I then put the template marker point cordinates into the configuration which were taken from the mri_ctf <br>
</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
<br>
</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg = [];</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.method = <span style="color:rgb(178,69,243)">'fiducial'</span>;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.target.pnt(1,:) = [91.1 3.0 49.2]./10;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.target.pnt(2,:) = [-0.1 70.5 0.0]./10;</div>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.target.pnt(3,:) = [0.1 -70.5 0.0]./10;</div>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier;min-height:12px">
<br class="m_-4831077437308618983webkit-block-placeholder">
</p>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
cfg.target.label = {<span style="color:rgb(178,69,243)">'NAS'</span> <span style="color:rgb(178,69,243)">
'LPA'</span> <span style="color:rgb(178,69,243)">'RPA'</span>};</div>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier;min-height:12px">
<br class="m_-4831077437308618983webkit-block-placeholder">
</p>
<p style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
</p>
<div style="margin:0px;font-size:10px;line-height:normal;font-family:courier">
grad_aligned = ft_sensorrealign(cfg, grad);</div>
</div>
<div><br>
</div>
<div>when I use ft_sensorrealign I get the following errors :</div>
<div><br>
</div>
<div>
<div>Undefined function or variable 'lab'.</div>
<div><br>
</div>
<div>Error in channelposition (line 314)</div>
<div>n = size(lab,2);</div>
<div><br>
</div>
<div>Error in ft_datatype_sens (line 328)</div>
<div> [chanpos, chanori, lab] = channelposition(sens);</div>
<div><br>
</div>
<div>Error in ft_sensorrealign (line 212)</div>
<div>elec_original = ft_datatype_sens(elec_<wbr>original); % ensure up-to-date sensor description (Oct 2011)</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>when I use ft_electroderealign I get the following errors: </div>
<div><br>
</div>
<div>
<div>Error using ft_fetch_sens (line 192)</div>
<div>no electrodes or gradiometers specified.</div>
<div><br>
</div>
<div>Error in ft_electroderealign (line 195)</div>
<div> elec_original = ft_fetch_sens(cfg);</div>
</div>
<div><br>
</div>
<div><br>
</div>
<div>Hope you can help me figure out why I'm getting these errors.</div>
<div>Thanks,</div>
<div>Ainsley </div>
</div></div></div>
______________________________<wbr>_________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a></div>
</blockquote>
</div>
<br>
</div>
<br>
<br>
<div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
J.M.Schoffelen, MD PhD<br>
Senior Researcher, VIDI-fellow - PI, language in interaction<br>
Telephone: <a href="tel:+31%2024%20361%204793" value="+31243614793" target="_blank">+31-24-3614793</a></div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Physical location: room 00.028</div>
<div style="color:rgb(0,0,0);letter-spacing:normal;text-align:start;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px;word-wrap:break-word">
Donders Centre for Cognitive Neuroimaging, Nijmegen, The Netherlands<br>
<br>
<br>
</div>
</div>
</div>
</div>
<br>
</div>
<br>______________________________<wbr>_________________<br>
fieldtrip mailing list<br>
<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a href="https://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">https://mailman.science.ru.nl/<wbr>mailman/listinfo/fieldtrip</a><br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div style="margin:0px;padding:0px;border:0px;font-family:Arial,Helvetica,Tahoma,sans-serif;font-size:12px;font-stretch:inherit;line-height:16px;vertical-align:baseline;color:rgb(64,63,71)"><b>Ainsley Temudo</b><br>Research Assistant </div><div style="margin:0px;padding:0px;border:0px;font-family:Arial,Helvetica,Tahoma,sans-serif;font-size:12px;font-stretch:inherit;line-height:16px;vertical-align:baseline;color:rgb(64,63,71)">Sreenivasan Lab<br>NYU Abu Dhabi<br>Office Tel (UAE): +971 2 628 4764<br>Mobile (UAE): +971 56 664 6952<br></div><span title="Saadiyat" style="margin:0px;padding:0px;border:0px;font-family:Arial,Helvetica,Tahoma,sans-serif;font-size:12px;font-stretch:inherit;line-height:16px;vertical-align:baseline;display:block;color:rgb(64,63,71)"><br>NYU Abu Dhabi, Saadiyat Campus<br>P.O. Box 129188<br>Abu Dhabi, United Arab Emirates</span></div></div>
</div>