<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">José,<div><br></div><div>Coregistration is a tricky thing, particularly if you start mixing results from two different software packages. I'd stick to one package, that's my recommendation, unless you really know what all individual steps are doing. Are you sure that your Aff_1 is doing what you think it is doing? E.g. does it apply to an anatomical volume with the same orientation, FOV, etc as the T1.nii?</div><div>Also, I think that for any automatic registration tool you use, it is necessary to get the geometric objects in approximate alignment, which means you need to select fiducials, otherwise your algorithm will not converge to the correct solution. I usually use ft_volumerealign twice. The first time to get an approximate registration (cfg.method = 'interactive'). If you have a headsurface determined with a polhemus device, you can call ft_volumerealign a second time (with the output to the first call as the input mri), in combination with cfg.method = 'headshape', and cfg.headshape = ft_read_headshape('headshapefile.txt')</div><div>Finally, I'd recommend not to re-post the same question too quickly after itself.</div><div><br></div><div>Best wishes,</div><div>Jan-Mathijs</div><div><br></div><div><br></div><div><br></div><div><br></div><div><div><div>On Apr 29, 2013, at 12:31 PM, José Ángel Pineda wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div dir="ltr"><div><div><div><div>Dear experts,<br><br>I was using manual selection of the fiducials in
order to get the affine transformation of the MRI T1 image to the MEG
sensor space.<br></div></div></div>Now, I have decided to use freesurfer for
obtaining the head surface and some function for performing an automatic
corregistration from head surface to fiducials (and polhemus
information), in order to avoid manual selection of the fiducials for each subject.<br><br>So I already have one affine transformation (Aff_1)<br><br></div><div>I
loaded the MRI T1 volume (mri = ft_read_mri(T1.nii)), I change the
mri.transform to mri.transform*Aff_1, but when I plot the results
(ft_determine_coordsys) I got what is in the attached snapshot.<br>
</div><div><br>Could you please give me any advice to solve this?<br><br>Thanks<br><br></div>cheers <br><br>Jose<br><br><span><image.png></span><br clear="all"><br>-- <br><div style="background-color:transparent"><div style="font-family: Times; font-size: medium; text-align: justify; margin-top: 0pt; margin-bottom: 0pt; "><span style="font-family:Arial;font-size:12px;white-space:pre-wrap">José Angel Pineda Pardo</span></div><div style="font-family: Times; font-size: medium; text-align: justify; margin-top: 0pt; margin-bottom: 0pt; ">
<span style="font-family:Arial;font-size:12px;white-space:pre-wrap">Center of Biomedical Technology (CTB)</span></div><div style="font-family: Times; font-size: medium; text-align: justify; margin-top: 0pt; margin-bottom: 0pt; "><span style="font-size:9pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Parque Científico y Tecnológico de la UPM</span></div><div style="font-family: Times; font-size: medium; text-align: justify; margin-top: 0pt; margin-bottom: 0pt; "><span style="font-size:9pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">Campus de Montegancedo</span></div><div style="font-family: Times; font-size: medium; text-align: justify; margin-top: 0pt; margin-bottom: 0pt; "><span style="font-size:9pt;font-family:Arial;color:rgb(0,0,0);background-color:transparent;font-weight:normal;font-style:normal;text-decoration:none;vertical-align:baseline;white-space:pre-wrap">28223 Pozuelo de Alarcón, Madrid, ES</span></div>
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Spam detection software, running on the system "<a href="http://brievenbus.science.ru.nl">brievenbus.science.ru.nl</a>", has<br>identified this incoming email as possible spam. The original message<br>has been attached to this so you can view it (if it isn't spam) or label<br>similar future email. If you have any questions, see<br><a href="mailto:postmaster@science.ru.nl">postmaster@science.ru.nl</a> for details.<br><br>Content preview: Dear experts, I was using manual selection of the fiducials<br> in order to get the affine transformation of the MRI T1 image to the MEG<br> sensor space. Now, I have decided to use freesurfer for obtaining the head<br> surface and some function for performing an automatic corregistration from<br> head surface to fiducials (and polhemus information), in order to avoid manual<br> selection of the fiducials for each subject. [...] <br><br>Content analysis details: (5.0 points, 5.0 required)<br><br> pts rule name description<br>---- ---------------------- --------------------------------------------------<br> 3.9 BAYES_99 BODY: Bayesian spam probability is 99 to 100%<br> [score: 0.9997]<br> 1.6 HTML_IMAGE_ONLY_28 BODY: HTML: images with 2400-2800 bytes of words<br> 0.0 HTML_MESSAGE BODY: HTML included in message<br>-1.0 RCVD_IN_DNSWL_LOW RBL: Sender listed at <a href="http://www.dnswl.org/">http://www.dnswl.org/</a>, low<br> trust<br> [209.85.128.179 listed in list.dnswl.org]<br> 0.6 DC_PNG_UNO_LARGO Message contains a single large inline gif<br> 0.0 DC_IMAGE_SPAM_TEXT Possible Image-only spam with little text<br> 0.0 DC_IMAGE_SPAM_HTML Possible Image-only spam<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</blockquote></div><br><div>
<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; font-size: medium; "><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; font-size: medium; "><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-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; font-size: medium; "><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; font-size: medium; "><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; font-size: medium; "><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-size: medium; 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></span></div></span></div></span></div></span></div></span></span>
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