<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div><br><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Kanal Eliezer <<a href="mailto:ekanal@cmu.edu">ekanal@cmu.edu</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">September 26, 2011 9:45:00 PM GMT+02:00<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">jan-mathijs schoffelen <<a href="mailto:jan.schoffelen@DONDERS.RU.NL">jan.schoffelen@DONDERS.RU.NL</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(0, 0, 0, 1);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>Re: [FieldTrip] source localization difficulties</b><br></span></div><br><div>Hello Dr Schoffelen -<br><br>Thanks for the advice. The way I got this part to work was to use SPM to convert my DICOM files to NIfTI ('*.img') and use `ft_read_mri` on that file, instead of reading the DICOM files directly. Using this method, I was able to reconstruct well.<br><br>However, it seems that there's another related issue. When running the<br><span class="Apple-tab-span" style="white-space:pre"> </span>ft_plot_sens(data_preprocessed.hdr.grad);<br><span class="Apple-tab-span" style="white-space:pre"> </span>hold on;<br><span class="Apple-tab-span" style="white-space:pre"> </span>ft_plot_vol(vol);<br>check, I got the attached image. Do you have any idea why it's doing that? Please let me know if I can provide any more details which could help troubleshoot. <br><br>In case it's relevant, I did notice that the output structure of the `ft_volumerealign` function (run with method='interactive') contained the following field:<br><span class="Apple-tab-span" style="white-space:pre"> </span>mri_realign.coordsys = 'ctf';<br>That can't be correct. I'm pretty sure it should be 'nifti'. However, I tried re-running `ft_volumesegment` after manually changing that value, and the figure looks the same.<br><br>Any help would be most appreciated! Thanks -<br><br>Elli<br><br><br><br><img id="d41d5ebe-449f-47e6-8f7e-5c116bdbb11e" height="401" width="543" apple-width="yes" apple-height="yes" src="cid:E5203989-C5CF-4494-A108-6491ECE763BC"><br>On Sep 24, 2011, at 3:09 AM, jan-mathijs schoffelen wrote:<br><br><blockquote type="cite">Hi Elli,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Hello Dr. Schoffelen -<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">I sent a response to the below email, but I think it got lost in the shuffle. I tried what you suggested, and I got the image attached below (matlab figure).<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Two questions: (1) What could be the cause of this poor alignment? This isn't right/left flipping, as the nose also looks to be in the back. (2) Do you have any idea why the reconstruction of the MRI looks so poor? FreeSurfer reconstructions looked much "healthier".<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">To combine both questions into 1 answer, I wouldn't say that the alignment is bad, it's the segmentation that seems to be completely off. This usually happens, when FieldTrip assigns the wrong coordinate system to the MRI. For the segmentation to work, SPM needs an approximate coregistration of the MRI in MNI-space. FieldTrip tries to achieve this, and needs the tag mri.coordsys for this. This tag is usually set after a pass through ft_volumerealign, where you can specify a cfg.coordsys (I just noticed this as an undocumented option: perhaps that needs to change). By default, this tag is set to 'ctf', see <a href="http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined">http://fieldtrip.fcdonders.nl/faq/how_are_the_different_head_and_mri_coordinate_systems_defined</a> for a definition of the coordinate systems. If the coordinate system in which the sensors are defined differs from the ctf coordinate system, causing a bad initial alignmnent prior to the segmentation and a worthless segmentation.<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">You mentioned below that I could simply load the up freesurfer files and go from there. All the *.mgz files I've found from freesurfer processing are simply volumetric MRI files. The surface files are stored in a variety of formats with seemingly no file extension. Is there a way to load FreeSurfer surfaces, or should I be using `ft_prepare_headmodel` to do that?<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">The ft_read_headshape function should be able to read freesurfer triangle and quadrangle files. Use it as ft_read_headshape(filename, 'fileformat', 'freesurfer-triangle_binary');<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><blockquote type="cite">Thanks -<br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite"><br></blockquote></blockquote><blockquote type="cite"><blockquote type="cite">Eliezer Kanal<br></blockquote></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Best,<br></blockquote><blockquote type="cite"><br></blockquote><blockquote type="cite">Jan-Mathijs<br></blockquote></div></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-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>Donders Institute for Brain, Cognition and Behaviour, <br>Centre for Cognitive Neuroimaging,<br>Radboud University Nijmegen, The Netherlands</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></span>
</div>
<br></body></html>