<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Hi Stan,<div><br></div><div>Part of the solution you’re looking for probably lies in the fact that both the forward and inverse warp are non-linear transformations (when the volumetric normalization is done with cfg.nonlinear = ‘yes’). In other words, the inverse warp cannot be achieved by a simple linear transformation (i.e. the (p)inv of a xxx.transform matrix). Fortunately, ft_warp_apply supports both ft_warp_apply(params, pos, ‘individual2sn’), and ft_warp_apply(params, pos, ‘sn2individual’). The latter aims to achieve the inverse warp you’re looking for. Probably you need to then also still apply the inverse of mri_realign_mni.initial.</div><div><br></div><div>Best,</div><div>JM</div><div><br></div><div><br><div><div>On Sep 22, 2014, at 5:12 PM, Stan van Pelt <<a href="mailto:s.vanpelt@psych.ru.nl">s.vanpelt@psych.ru.nl</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Eelke,<br><br>Thanks a lot, I seem to have missed that thread, very informative!<br>However, I seem not able yet to do the inverse warping, from MNI-coordinates <br>to CTF-coordinates.<br><br>- First I do<br>mri_realign_mni=ft_volumenormalise([],mri_realign)<br><br>- This gives me the transformation/normalization parameters from ctf->mni<br>- As an example, I apply them to a random coordinate, here [3 5 6]:<br>mnipos=ft_warp_apply(mri_realign_mni.params,ft_warp_apply(mri_realign_mni.initial,[3 <br>5 6]),'individual2sn')<br><br>- This gives me mni-coordinates -6.0652 -21.7174 -57.2273<br>- But how can I do the reverse?<br>- If I do<br>round(ft_warp_apply(pinv(mri_realign_mni.transform),mnipos))<br> I don't get [3 5 6]<br><br>- It seems to me I should do something like<br>ctfpos=ft_warp_apply(pinv(mri_realign_mni.params, <br>mnipos),mnipos,'individual2sn')<br> or so, but I am not getting it right...<br><br>Best,<br>Stan<br><br><br>-----Original Message-----<br>From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> <br>[<a href="mailto:fieldtrip-bounces@science.ru.nl">mailto:fieldtrip-bounces@science.ru.nl</a>] On Behalf Of Eelke Spaak<br>Sent: maandag 22 september 2014 13:20<br>To: FieldTrip discussion list<br>Subject: Re: [FieldTrip] leadfields MNI-coordinates<br><br>Hi Stan,<br><br>Have a look at this recent thread on the list (4 messages, Tom and me, this <br>is the starting message):<br><a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2014-August/008362.html">http://mailman.science.ru.nl/pipermail/fieldtrip/2014-August/008362.html</a><br>I think that might help you.<br><br>Groetjes,<br>Eelke<br><br>On 22 September 2014 12:44, Stan van Pelt <<a href="mailto:s.vanpelt@psych.ru.nl">s.vanpelt@psych.ru.nl</a>> wrote:<br><blockquote type="cite">Dear FieldTrippers,<br><br><br><br>For sourceconstruction (CTF275 MEG data) at specific ROIs, I want to<br>compute leadfields at specific (MNI-)coordinates in the brain. I am<br>trying to find out how that is most easily done using FieldTrip<br><br><br><br>- The most intuitive way seems to me to warp the MNI template to the<br>individual’s brain<br>(<a href="http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_">http://fieldtrip.fcdonders.nl/example/create_single-subject_grids_in_</a><br>individual_head_space_that_are_all_aligned_in_mni_space)<br>, and then apply the warping parameters to the ROI’s MNI-coordinates,<br>and enter the subsequent CTF-coordinates into ft_prepare_leadfield.<br>However, I am not sure where exactly I can find these parameters, and<br>how to apply them. Are these the ones in [gridsrc].params (output <br>ft_sourcemodel)?<br><br>- Alternatively, should I run ft_volumenormalise to warp the brain to<br>MNI-space, and then inversely apply the warping parameters to the<br>ROI’s MNI-coordinates? Again, where can I find the warping parameters<br>in this case, and how should they be applied?<br><br><br><br>Best,<br><br>Stan<br><br><br><br>-<br>Stan van Pelt, PhD<br>Donders Institute for Brain, Cognition and Behaviour Centre for<br>Cognition Montessorilaan 3, B.01.34<br>6525 HR Nijmegen, the Netherlands<br>tel: +31 24 3616288<br><br><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br></blockquote><br>_______________________________________________<br>fieldtrip mailing list<br><a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip<br>_______________________________________________<br>fieldtrip mailing list<br>fieldtrip@donders.ru.nl<br>http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</blockquote></div><br><div apple-content-edited="true">
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-webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-border-horizontal-spacing: 0px; -webkit-border-vertical-spacing: 0px; -webkit-text-decorations-in-effect: none; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div>Jan-Mathijs Schoffelen, MD PhD </div><div><br></div><div>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</div><div><br></div><div>Max Planck Institute for Psycholinguistics,</div><div>Nijmegen, The Netherlands</div><div><br></div><div><a href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div><div>Telephone: +31-24-3614793</div><div><br></div><div><a href="http://www.hettaligebrein.nl">http://www.hettaligebrein.nl</a></div></div></span></div></span></div></span></div></span></div></span></div></span></div></span></div></span></span>
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