<html><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">Dear David,<div><br></div><div>This is a good point. As far as I can see from the code, no distinction is made between gradiometers and magnetometers.</div><div>Naively, I would propose the following: first indeed split the data into two subset: gradiometers only and magnetometers only, only then apply the channel reparation routine. Yet, for the gradiometer subset data, it is questionable whether as such the replacement of a bad channel with its neighbours makes sense, because this would lead to averaging gradients of the magnetic field with an orthogonal orientation.</div><div> </div><div>In other words, this is probably not the most sensible approach. I don't think repairing after combining the planar gradients is desired, because this leads to an unwanted amplification of the noise (because the combination step results in taking an absolute value). Alternatively, you could consider using ft_megrealign, which in principle could be used to repair bad channels. The recipe would be to only use the data with the clean channels in the input, and you would want to interpolate the data back onto the original sensor-array. An example for interpolating between two types of CTF-systems is shown here <a href="http://fieldtrip.fcdonders.nl/example/megrealign">http://fieldtrip.fcdonders.nl/example/megrealign</a>.</div><div><br></div><div>Just out of curiosity: doesn't the maxfilter in the Neuromag software allow for similar things?</div><div><br></div><div>Best wishes,</div><div><br></div><div>Jan-Mathijs </div><div><br><div><div>On Oct 21, 2010, at 9:49 PM, David Ziegler wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><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: 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 bgcolor="#ffffff" text="#000000"><font face="Georgia">Hi Fieldtrippers,<br><br>I would like to use ft_channelrepair to interpolate data for some missing/deleted channels with Neuromag 306 data. I am just wondering whether there are any potential problems with using the nearest neighbor interpolation, given the triplet format of the Neuromag system (two planar gradiometers and one magnetometer). <span class="Apple-converted-space"> </span><br><br>If this is problematic, are there other options to fixing bad/missing channels (e.g., can ft_channelrepair be run on just a subset of the channels, say the gradiometers after I run ft_combineplanar)?<br><br>Thanks!<br>David<br><br></font><font face="Georgia"></font><div class="moz-signature">--<span class="Apple-converted-space"> </span><br><div class="Section1" style="page: Section1; "><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-size: 11pt; font-family: 'Bodoni MT'; ">David A. Ziegler</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-size: 11pt; font-family: 'Bodoni MT'; ">Department of Brain and Cognitive Sciences<span class="Apple-converted-space"> </span><br>Massachusetts Institute of Technology<span class="Apple-converted-space"> </span><br>43 Vassar St<span class="GramE">,<span> <span class="Apple-converted-space"> </span></span>46</span>-5121<span class="Apple-converted-space"> </span><br>Cambridge, MA 02139</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-size: 11pt; font-family: 'Bodoni MT'; ">Tel: 617-258-0765</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-size: 11pt; font-family: 'Bodoni MT'; ">Fax: 617-253-1504</span></div><div style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-size: 11pt; font-family: 'Bodoni MT'; "><a href="mailto:daz@mit.edu" style="color: blue; text-decoration: underline; ">daz@mit.edu</a></span></div><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-family: Garamond; "> </span></p><p class="MsoNormal" style="margin-top: 0in; margin-right: 0in; margin-bottom: 0.0001pt; margin-left: 0in; font-size: 12pt; font-family: 'Times New Roman'; "><span style="font-family: Garamond; "> </span></p></div></div><p>--------------------------------------------------------------------------- You are receiving this message because you are subscribed to<span class="Apple-converted-space"> </span><br>the FieldTrip list. The aim of this list is to facilitate the discussion<span class="Apple-converted-space"> </span><br>between users of the FieldTrip toolbox, to share experiences<span class="Apple-converted-space"> </span><br>and to discuss new ideas for MEG and EEG analysis.<span class="Apple-converted-space"> </span><br>See also<span class="Apple-converted-space"> </span><a href="http://listserv.surfnet.nl/archives/fieldtrip.html" style="color: blue; text-decoration: underline; ">http://listserv.surfnet.nl/archives/fieldtrip.html</a><span class="Apple-converted-space"> </span><br>and<span class="Apple-converted-space"> </span><a href="http://www.ru.nl/neuroimaging/fieldtrip" style="color: blue; text-decoration: underline; ">http://www.ru.nl/neuroimaging/fieldtrip</a>.<br>---------------------------------------------------------------------------</p></div></span></blockquote></div><br><div apple-content-edited="true"> <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: 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-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>Dr. J.M. (Jan-Mathijs) Schoffelen </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: 0031-24-3614793</div></div></span></div></span> </div><br></div></body></html><p>---------------------------------------------------------------------------
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