<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear Hanneke,<div><br></div><div>The information stored in dig can indeed be read into fieldtrip; this is done by read_headshape, which reads in all the points and classifies them as fiducial (i.e. nasion/LPA/RPA), stored in shape.fid, or other, stored in shape.pnt. shape.pnt would therefore include your HPI coils and additional digitised points (and any digitised EEG sensor locations if you collected EEG also). </div><div><br></div><div>As you're probably aware, there are two registrations that need to take place - the first is the registration of coil locations to sensor locations, and the second is the registration of the subject's MR scan to the coil locations/fiducials. The first is done at the time of recording (i.e. it is HPI); the sensors are by default read into fieldtrip using the same co-ordinates as the coils/digitised points (i.e. head coordinates rather than sensor coordinates, done by mne2grad in read_header). The second is done by fieldtrip, and is the registration of coil locations to the MR scan. This means that you wouldn't be able to improve the registration of coils etc. to the sensors (this registration has been done already by the HPI), but what you might be able to do is to use the additional points to improve the registration of the coil locations to the subject's MR scan. Typically they should be located on the scalp, and by minimising the mean squared error of the distance between coil locations/other digitised points and scalp you should be able to get a good registration.</div><div><br></div><div>Unfortunately I'm not quite sure how or whether fieldtrip does this; I'm afraid I use fieldtrip mainly to read the data into SPM (which does allow you to use these additional points to aid registration to the subject's scalp surface). But I imagine fieldtrip is able to do this also, and perhaps someone who knows more about fieldtrip could explain how to use the information in read_headshape to achieve this?</div><div><br></div><div>Hope this helps,</div><div>Laurence</div><div><br></div><div><br></div><div><div>
<span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: 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: 0; "><span class="Apple-style-span" style="border-collapse: separate; color: rgb(0, 0, 0); font-family: Helvetica; font-size: 12px; 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-size: 12px; 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-size: 12px; 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 class="AppleMailSignature" id="17D31EC3-297A-4FA6-B7EE-EE06DE0A8243"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">===========================================</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Laurence Hunt, DPhil Student</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "> Centre for Functional MRI of the Brain (FMRIB), </div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">University of Oxford</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; "><a href="mailto:lhunt@fmrib.ox.ac.uk">lhunt@fmrib.ox.ac.uk</a></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">Phone: (+44)1865-(2)22738</div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px; ">===========================================</div></div></div></div></div></span></div></span></div></span></span>
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<br><div><div>On 18 Nov 2009, at 12:38, Hanneke Van Dijk wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
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<!-- Converted from text/plain format --><p><font size="2">Dear all,<br>
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In my group we have a question regarding the use of the coil locations and/ or isotrack data to do source analysis. We are doing data analysis using FT and the MNE toolbox, on a dataset recorded with a Neuromag122 system.<br>
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The four coils were placed in different locations then in the CTF system, which uses the anatomical landmarks (left ear, right ear and nasion). Here we placed the coils on the scalp; two approximately above the eyes and two behind the ears. We digitized the locations of the coils using the polhemus, togheter with the anatomical landmarks and some more points. We would very much like to know HOW and WHERE fieldtrip uses the coil-location information and if it is possible to use the polhemus data as well, to place the head at the correct location within the helmet and to do sourceanalysis.<br>
<br>
I noticed allready that when reading the fiff file with 'fiff_read_meas_info' (MNE) there is a field called .dig which seems to contain the coordinates of digitized locations. I have no idea though how to integrate this information into the data so fieldtrip can use it.<br>
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Thanks in advance for any information,<br>
<br>
Hanneke van Dijk<br>
<br>
Institute for Clinical Neuroscience and Medical Psychology,<br>
Heinrich Heine Universitaet, Duesseldorf.<br>
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<p>----------------------------------</p><p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p><p> <a href="http://listserv.surfnet.nl/archives/fieldtrip.html">http://listserv.surfnet.nl/archives/fieldtrip.html</a></p><p> <a href="http://www.ru.nl/fcdonders/fieldtrip/">http://www.ru.nl/fcdonders/fieldtrip/</a></p>
</blockquote></div><br></div></body></html><p>----------------------------------</p>
<p>The aim of this list is to facilitate the discussion between users of the FieldTrip toolbox, to share experiences and to discuss new ideas for MEG and EEG analysis.</p>
<p> http://listserv.surfnet.nl/archives/fieldtrip.html</p>
<p> http://www.ru.nl/fcdonders/fieldtrip/</p>