<html>
<head>
<meta content="text/html; charset=ISO-8859-1"
http-equiv="Content-Type">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<div class="moz-cite-prefix">Hi Ye,<br>
<br>
could the problem be related to setting a wrong (or no) coordinate
system? I am not an expert in anatomical preprocessing, but to me
it seems that volumereslice assumes a false origin, thereby
'moving' the brain out of the picture. Also your first pictures
you sent seem to me like a coordinate mismatch.<br>
<br>
Additionally, as you suggested, I think volumereslice is not
necessary at all. It already looks fine beforehands and obviously,
you do not specify any parameter, so why use it after all? I'd try
to do it without ft_volumereslice, but check what coordinate
system you are in, e.g. use ft_determine_coordsys(mri) after
reading in your mri. <br>
<br>
Best,<br>
Jörn<br>
<br>
<br>
On 3/6/2013 10:35 PM, Ye Mei wrote:<br>
</div>
<blockquote cite="mid:5137B6B9.5080400@gmail.com" type="cite">Hi
Jan-Mathijs,
<br>
<br>
Thank you very much for the reply.
<br>
<br>
I think the problem starts at "mri_sliced = ft_volumereslice([],
mri);" before using "ft_volumesegment.".
<br>
<br>
The attached file "beforevolumnslice.png" is the result of
"imagesc(squeeze(mri.anatomy(:,111,:)))";
<br>
The attached file "aftervolumnslice.png" is the result of
"imagesc(squeeze(mri_sliced.anatomy(:,111,:)))".
<br>
<br>
We can see part of the head in "aftervolumnslice.png" is already
sliced away.
<br>
<br>
Could one do source localization without using "mri_sliced =
ft_volumereslice([], mri);"?
<br>
<br>
To circumvent the problem, I am trying to use FreeSurfer instead
of ft_volumereslice and ft_volumesegment. I had several .mgz files
from freesurfer.
<br>
Can I do the following?
<br>
--------
<br>
mri=ft_read_mri("brain.mgz"); %brain.mgz is the segmented brain by
FreeSurfer
<br>
<br>
cfg = [];
<br>
cfg.method ='fiducial';
<br>
cfg.fiducial.nas = [30 132 96];% position of Nasion
<br>
cfg.fiducial.lpa = [127 113 170];% position of LPA
<br>
cfg.fiducial.rpa = [125 115 18]% position of RPA
<br>
cfg.fiducial.zpoint = [125 125 220]
<br>
[mri_aligned] = ft_volumerealign(cfg, mri);
<br>
<br>
cfg = [];
<br>
cfg.method = 'singleshell';
<br>
vol = ft_prepare_headmodel(cfg, mri_aligned);
<br>
...
<br>
---------
<br>
<br>
thanks ahead,
<br>
Ye
<br>
<br>
<br>
On 13-02-28 05:10 PM, <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> wrote:
<br>
<blockquote type="cite">Send fieldtrip mailing list submissions to
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit
<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>
<br>
or, via email, send a message with subject or body 'help' to
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>
<br>
<br>
You can reach the person managing the list at
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-owner@science.ru.nl">fieldtrip-owner@science.ru.nl</a>
<br>
<br>
When replying, please edit your Subject line so it is more
specific
<br>
than "Re: Contents of fieldtrip digest..."
<br>
<br>
<br>
Today's Topics:
<br>
<br>
1. Re: NIHC-BrainGain Tutorial Day - March 21, 2013
<br>
(Robert Oostenveld)
<br>
2. Re: segmented brain seems not fitting the sensor
helmet well
<br>
(jan-mathijs schoffelen)
<br>
3. Re: segmented brain seems not fitting the sensor
helmet well
<br>
(Ye Mei)
<br>
<br>
<br>
----------------------------------------------------------------------
<br>
<br>
Message: 1
<br>
Date: Thu, 28 Feb 2013 17:46:39 +0100
<br>
From: Robert Oostenveld <a class="moz-txt-link-rfc2396E" href="mailto:r.oostenveld@donders.ru.nl"><r.oostenveld@donders.ru.nl></a>
<br>
To: FieldTrip discussion list <a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip@science.ru.nl"><fieldtrip@science.ru.nl></a>
<br>
Subject: Re: [FieldTrip] NIHC-BrainGain Tutorial Day - March 21,
2013
<br>
Message-ID:
<a class="moz-txt-link-rfc2396E" href="mailto:9741C083-F00A-4BC9-86EF-FB99715576A7@donders.ru.nl"><9741C083-F00A-4BC9-86EF-FB99715576A7@donders.ru.nl></a>
<br>
Content-Type: text/plain; charset=windows-1252
<br>
<br>
Dear FieldTrip users,
<br>
<br>
The NIHC-BrainGain Tutorial Day marks the end of the BrainGain
project. For the last 6 years, the development and continued
support of FieldTrip for normal/offline and realtime/online
analysis has received support from the BrainGain project.
<br>
<br>
There is now more information available online on this tutorial
day, please see
<br>
<a class="moz-txt-link-freetext" href="https://www.hersenenencognitie.nl/contents/1876">https://www.hersenenencognitie.nl/contents/1876</a>
<br>
<a class="moz-txt-link-freetext" href="https://www.hersenenencognitie.nl/contents/1915">https://www.hersenenencognitie.nl/contents/1915</a>
<br>
<br>
If you happen to be close to Nijmegen, you might also want to
come to the "Breinfest" on Tuesday evening 19 March in the city
centre with talks by international speakers and BCI demo's for
the general public. Personally, I will be demonstrating how
real-time data streaming and processing can be done using the
FieldTrip buffer to various platforms (OS X, WIndows, Linux), to
the Raspberry Pi and even to an Arduino (yes, fieldtrip runs on
an arduino! ... well, a small part of it runs on an arduino).
See <a class="moz-txt-link-freetext" href="http://www.ru.nl/breinfest">http://www.ru.nl/breinfest</a> for details on the evening.
<br>
<br>
best regards,
<br>
Robert
<br>
<br>
<br>
<br>
On 19 Feb 2013, at 14:30, Robert Oostenveld wrote:
<br>
<br>
<blockquote type="cite">NIHC-BrainGain Tutorial Day:
<br>
Tools and novelties in neurotechnology research
<br>
We invite PhD students, post-docs and senior researchers
working in the fields of brain-computer interfacing (BCI),
neurofeedback, cognitive neuroscience, neuroinformatics,
neurosurgery and related topics to our Tutorial Day on March
21st, 2013 in the Sanadome Nijmegen.
<br>
The day marks the end of the BrainGain consortium, a six-year
joint-effort project on Brain-Computer Interfacing and related
technologies. More information on BrainGain can be found here.
<br>
The Tutorial Day will consist of a 'tools' track and a
'novelties? track. The 'tools' track is intended to provide
both newcomers to the field and experienced researchers with
an overview of the tools needed to integrate cognitive
neuroscience and advanced invasive and non-invasive
technology. Topics range from data streaming to modelling and
statistics, and from online fMRI decoding to a crash course in
neuroethics., You will also receive some helpful insights for
a future career, in case you are interested in applying for a
grant in the near future or considering setting up your own
company.
<br>
The 'novelties' track covers a wide range of topics indicating
some of the possible topics to be further explored in BCI and
neurotechnology research, including genetics, robotics and
intracranial recordings.
<br>
There is no need to stick to one of the two tracks the whole
day: you are free to switch between tracks any time.
<br>
In parallel to the lectures, there will be several
interesting demonstrations.
<br>
The full programme and registration form can be found on the
NIHC website (<a class="moz-txt-link-freetext" href="https://www.hersenenencognitie.nl">https://www.hersenenencognitie.nl</a>). Please
register before 1 March 2013. Participation is free. Lunch and
drinks will be provided.
<br>
We hope to welcome you on March 21st in Nijmegen!
<br>
Susanna Bicknell
<br>
Radboud University Nijmegen
<br>
____________________________________________________________________
<br>
Faculty of Science | Finance and Economic Affairs | Project
Management | LC-IMPACT
<br>
Faculty of Social Sciences | Donders Centre for Cognition |
BRAINGAIN | Project Manager
<br>
T +31 24 3653300 | HG00.616 (Monday, Thursday)
<br>
Faculty of Science | IMAPP | T +31 24 3652972 | HG07.315
(Tuesday, Wednesday)
<br>
Postal address: P.O. Box 9010, 6500 GL Nijmegen, The
Netherlands
<br>
Visiting and courier service address: Heyendaalseweg 135, 6525
AJ Nijmegen, The Netherlands
<br>
<br>
_______________________________________________
<br>
fieldtrip mailing list
<br>
<a class="moz-txt-link-abbreviated" 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>
<br>
</blockquote>
<br>
<br>
<br>
------------------------------
<br>
<br>
Message: 2
<br>
Date: Thu, 28 Feb 2013 18:54:14 +0100
<br>
From: jan-mathijs schoffelen
<a class="moz-txt-link-rfc2396E" href="mailto:jan.schoffelen@donders.ru.nl"><jan.schoffelen@donders.ru.nl></a>
<br>
To: FieldTrip discussion list <a class="moz-txt-link-rfc2396E" href="mailto:fieldtrip@science.ru.nl"><fieldtrip@science.ru.nl></a>
<br>
Subject: Re: [FieldTrip] segmented brain seems not fitting the
sensor
<br>
helmet well
<br>
Message-ID:
<a class="moz-txt-link-rfc2396E" href="mailto:B86193FA-0829-494E-A52B-69955F3EAEBF@donders.ru.nl"><B86193FA-0829-494E-A52B-69955F3EAEBF@donders.ru.nl></a>
<br>
Content-Type: text/plain; charset="us-ascii"
<br>
<br>
Hi Ye,
<br>
<br>
Looks like a coregistration problem to me. In other words,
something went wrong in ft_volumesegment, because the images
were not sufficiently aligned. You need to investigate the input
and output of ft_volumesegment.
<br>
Do you use ft_volumerealign after calling ft_volumesegment? This
should be the other way around.
<br>
<br>
Best,
<br>
<br>
Jan-Mathijs
<br>
<br>
<br>
On Feb 28, 2013, at 5:38 PM, Ye Mei wrote:
<br>
<br>
<blockquote type="cite">Hello FieldtripList,
<br>
<br>
After segmentation and alignment using
<br>
'ft_volumesegment' and 'ft_volumerealign', one of the
subjects' segmented
<br>
brain seems rotated forward in the sensor helmet(brain.png)
and the
<br>
cerebellum part seems to be segmented out. However, his head
MRI seems
<br>
fitting the sensor helmet well(head.jpg). My another subject's
brain
<br>
seem to be correctly segmented without missing the cerebellum
part. And
<br>
the brain is not rotated forward.
<br>
<br>
Could might be the problem?
<br>
<br>
thanks ahead,
<br>
Ye
<br>
<brain.png><head.jpg>_______________________________________________
<br>
fieldtrip mailing list
<br>
<a class="moz-txt-link-abbreviated" 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>
<br>
</blockquote>
Jan-Mathijs Schoffelen, MD PhD
<br>
<br>
Donders Institute for Brain, Cognition and Behaviour,
<br>
Centre for Cognitive Neuroimaging,
<br>
Radboud University Nijmegen, The Netherlands
<br>
<br>
Max Planck Institute for Psycholinguistics,
<br>
Nijmegen, The Netherlands
<br>
<br>
<a class="moz-txt-link-abbreviated" href="mailto:J.Schoffelen@donders.ru.nl">J.Schoffelen@donders.ru.nl</a>
<br>
Telephone: +31-24-3614793
<br>
<br>
-------------- next part --------------
<br>
An HTML attachment was scrubbed...
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/e027b4fb/attachment-0001.html"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/e027b4fb/attachment-0001.html></a><br>
<br>
------------------------------
<br>
<br>
Message: 3
<br>
Date: Thu, 28 Feb 2013 17:09:57 -0500
<br>
From: Ye Mei <a class="moz-txt-link-rfc2396E" href="mailto:frank.ye.mei@gmail.com"><frank.ye.mei@gmail.com></a>
<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
<br>
Subject: Re: [FieldTrip] segmented brain seems not fitting the
sensor
<br>
helmet well
<br>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:512FD5B5.8080700@gmail.com"><512FD5B5.8080700@gmail.com></a>
<br>
Content-Type: text/plain; charset="iso-8859-1"; Format="flowed"
<br>
<br>
Hello All,
<br>
<br>
I found the problem I mentioned in the previous email was caused
by
<br>
using "mri_sliced = ft_volumereslice([], mri);" before using
<br>
ft_volumesegment.
<br>
After erasing the line "mri_sliced = ft_volumereslice([],
mri);", the
<br>
segmented brain seems to be normal and fits the sensor helmet
well now,
<br>
as show in the attached figure(notvolumnsliced.jpg).
<br>
For another of my subject, if the "ft_volumereslice" is
included, the
<br>
brain looks sliced on the top(subject2vs.jpg). If no
"ft_volumreslice"
<br>
it looks normal(subject2.jpg).
<br>
<br>
I notice in the fieldtrip headmodel tutorial
<br>
(<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg">http://fieldtrip.fcdonders.nl/tutorial/headmodel_meg</a>),
<br>
"ft_volumereslice" is not used. but in the field trip beamformer
<br>
tutorial(<a class="moz-txt-link-freetext" href="http://fieldtrip.fcdonders.nl/tutorial/beamformer">http://fieldtrip.fcdonders.nl/tutorial/beamformer</a>), it
is used.
<br>
<br>
I am wondering if I should include "ft_volumereslice" in my
source
<br>
localization code. Can anyone give me some suggestions?
<br>
<br>
<br>
<br>
thanks ahead,
<br>
Ye
<br>
<br>
<br>
<br>
<br>
On 13-02-28 11:45 AM, <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> wrote:
<br>
<blockquote type="cite">Send fieldtrip mailing list submissions
to
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
<br>
<br>
To subscribe or unsubscribe via the World Wide Web, visit
<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>
<br>
or, via email, send a message with subject or body 'help' to
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>
<br>
<br>
You can reach the person managing the list at
<br>
<a class="moz-txt-link-abbreviated" href="mailto:fieldtrip-owner@science.ru.nl">fieldtrip-owner@science.ru.nl</a>
<br>
<br>
When replying, please edit your Subject line so it is more
specific
<br>
than "Re: Contents of fieldtrip digest..."
<br>
<br>
<br>
Today's Topics:
<br>
<br>
1. segmented brain seems not fitting the sensor helmet
well (Ye Mei)
<br>
<br>
<br>
----------------------------------------------------------------------
<br>
<br>
Message: 1
<br>
Date: Thu, 28 Feb 2013 11:38:21 -0500
<br>
From: Ye Mei <a class="moz-txt-link-rfc2396E" href="mailto:frank.ye.mei@gmail.com"><frank.ye.mei@gmail.com></a>
<br>
To: <a class="moz-txt-link-abbreviated" href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>
<br>
Subject: [FieldTrip] segmented brain seems not fitting the
sensor
<br>
helmet well
<br>
Message-ID: <a class="moz-txt-link-rfc2396E" href="mailto:512F87FD.80500@gmail.com"><512F87FD.80500@gmail.com></a>
<br>
Content-Type: text/plain; charset="iso-8859-1";
Format="flowed"
<br>
<br>
Hello FieldtripList,
<br>
<br>
After segmentation and alignment using
<br>
'ft_volumesegment' and 'ft_volumerealign', one of the
subjects' segmented
<br>
brain seems rotated forward in the sensor helmet(brain.png)
and the
<br>
cerebellum part seems to be segmented out. However, his head
MRI seems
<br>
fitting the sensor helmet well(head.jpg). My another subject's
brain
<br>
seem to be correctly segmented without missing the cerebellum
part. And
<br>
the brain is not rotated forward.
<br>
<br>
Could might be the problem?
<br>
<br>
thanks ahead,
<br>
Ye
<br>
-------------- next part --------------
<br>
A non-text attachment was scrubbed...
<br>
Name: brain.png
<br>
Type: image/png
<br>
Size: 15197 bytes
<br>
Desc: not available
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.png"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.png></a><br>
-------------- next part --------------
<br>
A non-text attachment was scrubbed...
<br>
Name: head.jpg
<br>
Type: image/jpeg
<br>
Size: 50294 bytes
<br>
Desc: not available
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.jpg"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/1d01f497/attachment.jpg></a><br>
<br>
------------------------------
<br>
<br>
_______________________________________________
<br>
fieldtrip mailing list
<br>
<a class="moz-txt-link-abbreviated" 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>
<br>
<br>
End of fieldtrip Digest, Vol 27, Issue 31
<br>
*****************************************
<br>
</blockquote>
-------------- next part --------------
<br>
A non-text attachment was scrubbed...
<br>
Name: notvolumnsliced.jpg
<br>
Type: image/jpeg
<br>
Size: 28621 bytes
<br>
Desc: not available
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment.jpg"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment.jpg></a><br>
-------------- next part --------------
<br>
A non-text attachment was scrubbed...
<br>
Name: subject2.jpg
<br>
Type: image/jpeg
<br>
Size: 27415 bytes
<br>
Desc: not available
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment-0001.jpg"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment-0001.jpg></a><br>
-------------- next part --------------
<br>
A non-text attachment was scrubbed...
<br>
Name: subject2vc.jpg
<br>
Type: image/jpeg
<br>
Size: 27788 bytes
<br>
Desc: not available
<br>
URL:
<a class="moz-txt-link-rfc2396E" href="http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment-0002.jpg"><http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20130228/d917ed81/attachment-0002.jpg></a><br>
<br>
------------------------------
<br>
<br>
_______________________________________________
<br>
fieldtrip mailing list
<br>
<a class="moz-txt-link-abbreviated" 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>
<br>
<br>
End of fieldtrip Digest, Vol 27, Issue 32
<br>
*****************************************
<br>
</blockquote>
<br>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
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
FieldTrip Development Team
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>