<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body bgcolor="#ffffff" text="#000000">
Hi,<br>
<br>
SInce the new updates (which should be available in the new FT
download version, see also the corresponding mail on the mailing
list), I would suggest to use a user-defined neighbourstructure,
verify this and then call channelrepair. E.g. try 'triangulation' as
a method - it might result in a better neighbourhood representation.<br>
Also, currently neighbourselection is using config settings first
before searching the data structure for sensor position information.
So if you define cfg.layout, it will definitely use the layout (so,
2D coordinates) instead of 3D coordinates defined in your data. This
might be suboptimal as well.<br>
<br>
Sorry for all the inconveniences. We will try to check why the
problem you got causes an issue and hopefully find a more generic
way to solve this. <br>
Jim, if not already done, it would be great if you followed
Jan-Mathijs' suggestion to provide further information such as
example data so that we can reproduce your problem and try to solve
it.<br>
Don, thanks for helping out ;)<br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 7/9/2011 12:57 AM, Rojas, Don ( Employee MEG-SOM ) wrote:
<blockquote
cite="mid:1B896C54-AEBC-4261-8A7A-7FC9E91FA6C6@ucdenver.edu"
type="cite">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:<br>
</div>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<div style="word-wrap: break-word;">
<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>
_______________________________________________
<div><br>
fieldtrip mailing list<br>
<a
moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl" target="_blank">fieldtrip@donders.ru.nl</a><br>
<a
moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></div>
</blockquote>
</div>
<br>
<div><span
style="word-spacing:
0px; font: medium
Helvetica;
text-transform: none;
color: rgb(0, 0, 0);
text-indent: 0px;
white-space: normal;
letter-spacing: normal;
border-collapse:
separate;"><span
style="word-spacing:
0px; font: medium
Helvetica;
text-transform: none;
color: rgb(0, 0, 0);
text-indent: 0px;
white-space: normal;
letter-spacing:
normal;
border-collapse:
separate;">
<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>
</span></span></div>
<br>
</div>
</div>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl"
target="_blank">fieldtrip@donders.ru.nl</a><br>
<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip"
target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
</blockquote>
</div>
<br>
_______________________________________________<br>
fieldtrip mailing list<br>
<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></blockquote>
</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>
</div>
</div>
_______________________________________________<br>
fieldtrip mailing list<br>
<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a moz-do-not-send="true"
class="moz-txt-link-freetext"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></blockquote>
</div>
<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>
_______________________________________________
fieldtrip mailing list
<a moz-do-not-send="true" class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a moz-do-not-send="true" class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
</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 moz-do-not-send="true" 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 moz-do-not-send="true" 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>
</div>
_______________________________________________<br>
fieldtrip mailing list<br>
<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a moz-do-not-send="true"
href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></blockquote>
</div>
<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-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;">
<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>
</span></span>
</div>
<br>
</div>
_______________________________________________<br>
fieldtrip mailing list<br>
<a moz-do-not-send="true"
href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></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-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; 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; font-size: medium;">
<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>
</span></span>
</div>
<br>
</div>
<pre wrap="">
<fieldset class="mimeAttachmentHeader"></fieldset>
_______________________________________________
fieldtrip mailing list
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>
<a class="moz-txt-link-freetext" href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a></pre>
</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>
</body>
</html>