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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Got it. Thank you very much.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#1F497D">Best - Don</span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> mne_analysis-bounces@nmr.mgh.harvard.edu [mailto:mne_analysis-bounces@nmr.mgh.harvard.edu]
<b>On Behalf Of </b>Matti Hamalainen<br>
<b>Sent:</b> Monday, April 18, 2016 12:00 PM<br>
<b>To:</b> Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b> Re: [Mne_analysis] mne_make_cor_set - transform problem<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi Don,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">In fact, the coordinate transformation between the scanner coordinates and surface RAS coordinates is in the file produced my mne_make_cor_set. <o:p></o:p></p>
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<p class="MsoNormal">You can see this when you do <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">mne_show_fiff —verbose —tag 222 —in <filename><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">To my understanding, it is only a displacement.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">- Matti<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Apr 18, 2016, at 11:53 AM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu">kriegerd@upmc.edu</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Hi Matti,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Thanks for responding so quickly.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I tried what you suggest for a scan for which I have dicoms.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I created 2 .fif’s, one with dicom_access and one with mne_make_cor_set.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Here are the two transforms grabbed with show_fiff:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># dicom_access</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># 222 = transform head -> MRI</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># 0.999356 0.028735 -0.021495</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># -0.035189 0.902169 -0.429945</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># 0.007038 0.430425 0.902599</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># -4.798210 8.148447 -50.913933 (inv. 5.440169 14.701207 49.355110)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># mne_make_cor_set</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># 222 = transform head -> MRI</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># 0.999505 0.024229 0.020096</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># -0.014078 0.915056 -0.403080</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># -0.028155 0.402598 0.914944</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"># -3.010607 -9.352709 -35.697933 (inv. 1.872374 23.003098 28.952219)</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">I guess the rotations look pretty much the same and if I apply the tkr2scanner transform to the displacement, -3.010607 -9.352709 -35.697933, I get</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-5.14 6.311 -52.083 which is also pretty good.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">That’s encouraging actually. Do you see any way to get it to kick out the correct displacements?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Don</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span class="apple-converted-space"><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> </span></span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""><a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mne_analysis-bounces@nmr.mgh.harvard.edu</a>
[<a href="mailto:mne_analysis-bounces@nmr.mgh.harvard.edu">mailto:mne_analysis-bounces@nmr.mgh.harvard.edu</a>]<span class="apple-converted-space"> </span><b>On Behalf Of<span class="apple-converted-space"> </span></b>Matti Hamalainen<br>
<b>Sent:</b><span class="apple-converted-space"> </span>Monday, April 18, 2016 11:36 AM<br>
<b>To:</b><span class="apple-converted-space"> </span>Discussion and support forum for the users of MNE Software<br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [Mne_analysis] mne_make_cor_set - transform problem</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Don,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">You can read the fif file mne_make_cor_set made in mrilab and do the coordinate transformation there as you have used to and produce a new fif file where the transformation is in place.<o:p></o:p></p>
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<p class="MsoNormal">This does not deal with the different coordinate systems between the one derived from the DICOM files and the mgz files, though.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">- Matti<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On Apr 18, 2016, at 11:31 AM, Krieger, Donald N. <<a href="mailto:kriegerd@upmc.edu"><span style="color:purple">kriegerd@upmc.edu</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">This is a follow-on to a previous post to which Jon Houck helpfully suggested using mne_make_cor_set.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I am using this to convert .mgz files to .fif .</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I normally start with the original dicom set and convert them to .fif using ELEKTA’s dicom_access.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">But for these MEG data sets, I only have a defaced (via freesurfer) .mgz files.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">In either case I then use the .fif files to do MEG coregistration with ELEKTA’s Mrilab tool.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Using Mrilab is part of my standard pipeline and I would like to stick with that if possible.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">When I convert a standard dicom scan series to fif using ELEKTA’s dicom_access, the .fif is in MR RAS coordinates.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">But a .fif file obtained by conversions from .mgz with mne_make_cor_set appears to be in tkr RAS coordinates instead.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">So the transform matrix that I get when I do the coregistration is: Head<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:Wingdings">à</span><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">tkrRAS
rather than Head<span class="apple-converted-space"> </span></span><span style="font-size:11.0pt;font-family:Wingdings">à</span><span class="apple-converted-space"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span></span><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">RAS
.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif""> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">I tried spoofing mne_make_cor_set with –talairach SomeOtherTransformation but Mrilab doesn’t appear to care.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">In addition, it’s not clear to me what transform to use even if it does work; maybe tkr2scanner .</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Any thoughts would be welcome and thanks.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif"">Best - Don</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"> <o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">---------<br>
<br>
Matti Hamalainen, Ph.D.<br>
Athinoula A. Martinos Center for Biomedical Imaging<br>
Massachusetts General Hospital<br>
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<a href="mailto:msh@nmr.mgh.harvard.edu"><span style="color:purple">msh@nmr.mgh.harvard.edu</span></a><br>
<a href="mailto:mhamalainen@partners.org"><span style="color:purple">mhamalainen@partners.org</span></a><br>
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<p class="MsoNormal"><span style="font-size:10.5pt;font-family:"Helvetica","sans-serif"">_______________________________________________<br>
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