<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">As a short follow up on this, the behavior of ft_neighbourplot is suspect only when supplying a cfg.neighbours field and plotting the result using the 2d layout file (as in the example I gave below), so this issue may not be the same as for the channel repair function. Using no layout file, the 3D plotted locations and labels appear to be correct. I can verify that the lower level functions called by ft_neighbourplot such as channelposition.m are returning the correct position and label info, but haven't had time to track the 2d plotting result down further. The neighbours returned by ft_neighbourselection also appear to be okay given a specified input distance.<div><br><div><div>On Jul 8, 2011, at 1:17 PM, Rojas, Don ( Employee MEG-SOM ) wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div bgcolor="#ffffff" text="#000000">Jörn, Jim et al.</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">There is indeed a general problem, most likely with channel indexing, in gradiometer systems. I think the data are read correctly with the low level functions, but functions like ft_channelrepair, ft_neighbourselection and ft_neighbourplot are not accounting for the locations correctly. I have attached a picture that I think illustrates this issue reasonably well. The following code was used t<span><neighbors.jpg></span>o generate this plot:</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">% read in data</div><div bgcolor="#ffffff" text="#000000">cfg = [];</div><div bgcolor="#ffffff" text="#000000">cfg.dataset = 'e,rfhp1.0Hz,COH';</div><div bgcolor="#ffffff" text="#000000">coh = ft_preprocessing(cfg);</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">% get neighbors and plot</div><div bgcolor="#ffffff" text="#000000">cfg = [];</div><div bgcolor="#ffffff" text="#000000">cfg.neighbourdist = .03;</div><div bgcolor="#ffffff" text="#000000">cfg.neighbours = ft_neighbourselection(cfg,coh);</div><div bgcolor="#ffffff" text="#000000">cfg.layout = '4D248.lay';</div><div bgcolor="#ffffff" text="#000000">ft_neighbourplot(cfg,coh);</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">You can see that the channel selected is labeled A216, which is incorrect - it should be A248. It's three neighbors are also incorrect (A208, A118 and A134 should probably be A195, A228 and A247).</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">I'm guessing this is the same indexing issue for gradiometers. Jan-Mathijs mentioned a fixed version of ft_channelrepair appearing today, so perhaps it will be the same problem and the fix can be propagated to these other functions.</div><div bgcolor="#ffffff" text="#000000"><br></div><div bgcolor="#ffffff" text="#000000">Don</div><div bgcolor="#ffffff" text="#000000"><br></div><div><div>On Jul 8, 2011, at 2:20 AM, Jörn M. Horschig wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">
<div bgcolor="#ffffff" text="#000000">
Dear Jim, Don and others,<br>
<br>
First of all, what Don suggested sounds indeed like the cause, if I
remember things correctly (with my limited experience). <br>
<br>
Anyhow, could one of you check ft_neighbourplot with the dataset and
the neighbourselection of choice? This allows you to see what
neighbours are selected for which sensors and where they lie in
space. If this looks fine, than the problem lies indeed in how
sensor position is deduced from the data structure.<br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 7/8/2011 9:11 AM, jan-mathijs schoffelen wrote:
<blockquote cite="mid:BB75D7D8-68AD-4466-8B52-CFB2BC90E66E@donders.ru.nl" type="cite">Dear Don,
<div><br>
</div>
<div>This sounds like a very likely cause of the problem. When we
wrote the 4D reading code at the time, we had the 248-channel
magnetometer system in mind. It could be that there are some
flaws related to the handling of gradiometers. This should not
only lead to (erratic) issues at the level of channelrepair, but
may also cause mayhem when doing planar gradient transformation,
or source reconstruction.</div>
<div>Would you happen to</div>
<div>1) feel like tackling this one with me, and improve FieldTrip
to deal with gradiometer systems correctly? </div>
<div><br>
</div>
<div>or</div>
<div><br>
</div>
<div>2) have a small gradiometer dataset which you can send to me
(e.g. through DropBox), so that I can look into it?</div>
<div><br>
</div>
<div>We can further discuss this off the discussion list.</div>
<div><br>
</div>
<div>Best wishes,</div>
<div><br>
</div>
<div>Jan-Mathijs</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On Jul 8, 2011, at 3:36 AM, Rojas, Don ( Employee MEG-SOM
) wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word;">Jim et al.
<div><br>
</div>
<div>In thinking about this further, it seems to me that
it is the indexing that is incorrect. The problem I
think is specific to gradiometer systems, which have two
(or more) locations per channel. The function appears to
assume that the sensor index based on the sens.label
field (only 1 per channel) will correspond 1 to 1 with
the sens.grad field (2 locations per channel), which is
not correct. So, my guess is that for first-order
gradiometer systems, the correct index for the sensor
location is 2x the index in the sens.label field.</div>
<div><br>
</div>
<div>So, in an example I have handy at home, the label
index for channel A234 is 107. Since I think Fieldtrip
stores gradiometer locations (by default) as:</div>
<div><br>
</div>
<div>Chn 1 lower coil x, y z</div>
<div>Chn 1 upper coil x, y z</div>
<div>Chn 2 lower coil x, y z</div>
<div>Chn 2 upper coil x, y z</div>
<div>.</div>
<div>.</div>
<div>.</div>
<div>Chn N</div>
<div><br>
</div>
<div>I think the correct position info for channel A234
would be found in sens.grad(214,:), not
sens.grad(107,:), which is what the ft_channelrepair
function chooses. So I think this is a bug in the
function specific to gradiometer systems.</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Don</div>
<div><br>
<div>
<div>On Jul 7, 2011, at 5:38 PM, Jim Li wrote:</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div>Thank you very much for confirming the problem,
Don, I appreciate it, :)</div>
<div> </div>
<div class="gmail_quote">Jim</div>
<div class="gmail_quote"> </div>
<div class="gmail_quote">On Thu, Jul 7, 2011 at 4:30
PM, Rojas, Don <span dir="ltr"><<a moz-do-not-send="true" href="mailto:Don.Rojas@ucdenver.edu" target="_blank">Don.Rojas@ucdenver.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex; margin: 0px 0px 0px
0.8ex; border-left: 1px solid rgb(204, 204,
204);">
<div style="word-wrap: break-word;">Jim,
<div><br>
</div>
<div>All I can do is confirm that this issue
exists for our 4D data as well, although we
don't use the ft_channelrepair function. The
same 4 quite distant channels (one had been
deleted in the dataset I had handy) were
chosen for repair when I ran this on one of
our datasets (also a 248 channel 4D system).
I agree the choice doesn't make any sense
given the 3 cm distance you define. A quick
look at the critical calculation in
ft_channelrepair, line 109 distance = ... is
correct given the inputs. So I wonder if the
issue is with the actual channel indices
used rather than the calculation, but I
don't have time to track that down. All I
can say is that for the distance you
specify, channels A235, A216, A199, A215
would be much closer to A234 than those that
are selected via the channel repair
function. Channel A8 is in fact nearly 21 cm
away from channel A234 in the array, based
on examination of the data read in from
Eugene Kronberg's pdf4D matlab object code,
which I think was originally the basis for
the FieldTrip 4D reader function.</div>
<div><br>
</div>
<div>Best,</div>
<div><br>
</div>
<div>Don Rojas</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<div>
<div>
<div>On Jul 7, 2011, at 1:26 PM, Jim
Li wrote:</div>
<br>
</div>
</div>
<blockquote type="cite">
<div>
<div>
<div>Dear Fieldtrip developer,</div>
<div> </div>
<div>Can anybody help me with this
channel-repair issue I've been
having? I can provide the raw data
if you need. I really want to
solve the problem, you know.</div>
<div> </div>
<div>Thanks a lot,</div>
<div> </div>
<div>Jim<br>
<br>
</div>
<div class="gmail_quote">On Thu, Jul
7, 2011 at 2:22 PM, Jim Li <span dir="ltr"><<a moz-do-not-send="true" href="mailto:megjim1@gmail.com" target="_blank">megjim1@gmail.com</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="padding-left: 1ex;
margin: 0px 0px 0px 0.8ex;
border-left: 1px solid rgb(204,
204, 204);">
<div>Hi Odelia,</div>
<div> </div>
<div>Yes, I downloaded the
latest version of Fieldtrip
and tried your suggestion
"cfg.neighbourdist = 0.03",
but it still weirdly uses the
far-away channels like A121 to
do the channel-repair for A234
(these two channels are
24.1172cm apart!). Here is
the detail:</div>
<div> </div>
<div>---------------------------</div>
<div>
<div>cfg
= [];<br>
cfg.dataset
= 'e,rfhp0.1Hz'; </div>
<div>cfg.trialdef.eventtype
= 'TRIGGER';<br>
cfg.trialdef.eventvalue
= 320; </div>
</div>
<div>
<div>cfg.trialdef.prestim
= 1;<br>
cfg.trialdef.poststim
= 1;<br>
cfg
= ft_definetrial(cfg);<br>
</div>
cfg.blc =
'yes';
% do baseline correction with
the complete trial
<div><br>
cfg.blcwindow
= [-1 0];<br>
cfg.channel
= {'MEG'};<br>
raw_DATA
= ft_preprocessing(cfg);</div>
</div>
<div> </div>
<div> </div>
<div>cfg = [];<br>
cfg.badchannel = {'A234'}; <br>
cfg.neighbourdist = 0.03;
<div><br>
[raw_DATA] =
ft_channelrepair(cfg,
raw_DATA)</div>
</div>
<div> </div>
<div>---------------------------------------------------------------------</div>
<div> </div>
<div>And here is the outcome:
-----------------------------</div>
<div>
<div><br>
the input is raw data with
248 channels and 201 trials<br>
repairing channel A234<br>
using neighbour A121<br>
using neighbour A143<br>
</div>
using neighbour A173<br>
using neighbour A8
<div><br>
repairing bad channels for
trial 1<br>
repairing bad channels for
trial 2<br>
repairing bad channels for
trial 3<br>
</div>
repairing bad channels for
trial 4<br>
repairing bad channels for
trial 5<br>
repairing bad channels for
trial 6<br>
repairing bad channels for
trial 7<br>
repairing bad channels for
trial 8<br>
repairing bad channels for
trial 9<br>
repairing bad channels for
trial 10</div>
<div>....</div>
<div> </div>
<div>-------------------------</div>
<div> </div>
<div>Thank you.</div>
<div> </div>
<font color="#888888">
<div>Jim<br>
</div>
</font></blockquote>
</div>
</div>
</div>
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<div style="word-wrap: break-word;">-----------------------<br>
Don Rojas, Ph.D.<br>
Associate Professor of Psychiatry<br>
U. of Colorado Denver Anschutz
Medical Campus<br>
Director, UCD
Magnetoencephalography Lab<br>
13001 E. 17th Pl F546<br>
Aurora, CO 80045<br>
<a moz-do-not-send="true" href="tel:303-724-4994" target="_blank" value="+13037244994">303-724-4994</a></div>
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</div>
<br>
<div>
<div style="word-wrap: break-word;">-----------------------<br>
Don Rojas, Ph.D.<br>
Associate Professor of Psychiatry<br>
U. of Colorado Denver Anschutz Medical Campus<br>
Director, UCD Magnetoencephalography Lab<br>
13001 E. 17th Pl F546<br>
Aurora, CO 80045<br>
303-724-4994</div>
</div>
<br>
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<br>
<div>
<span class="Apple-style-span" style="border-collapse: separate; 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; font-size: medium; "><span class="Apple-style-span" style="border-collapse: separate; 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; ">
<div style="word-wrap: break-word;">
<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 moz-do-not-send="true" href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a></div>
<div>Telephone: 0031-24-3614793</div>
</div>
</span></span>
</div>
<br>
</div>
<pre wrap=""><fieldset class="mimeAttachmentHeader"></fieldset>
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</blockquote>
<br>
<br>
<pre class="moz-signature" cols="72">--
Jörn M. Horschig
PhD Student
Donders Institute for Brain, Cognition and Behaviour
Centre for Cognitive Neuroimaging
Radboud University Nijmegen
Neuronal Oscillations Group
P.O. Box 9101
NL-6500 HB Nijmegen
The Netherlands
Contact:
E-Mail: <a class="moz-txt-link-abbreviated" href="mailto:jm.horschig@donders.ru.nl">jm.horschig@donders.ru.nl</a>
Tel: +31-(0)24-36-68493
Web: <a class="moz-txt-link-freetext" href="http://www.ru.nl/donders">http://www.ru.nl/donders</a>
Visiting address:
Trigon, room 2.30
Kapittelweg 29
NL-6525 EN Nijmegen
The Netherlands</pre>
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<span class="Apple-style-span" style="border-collapse: separate; 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; "><span class="Apple-style-span" style="border-collapse: separate; 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; ">-----------------------<br>Don Rojas, Ph.D.<br>Associate Professor of Psychiatry<br>U. of Colorado Denver Anschutz Medical Campus<br>Director, UCD Magnetoencephalography Lab<br>13001 E. 17th Pl F546<br>Aurora, CO 80045<br>303-724-4994</div></span></span>
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