<div dir="ltr"><div class="gmail_default" style="font-family:verdana,sans-serif">Dear Rajat,<br></div><div class="gmail_default" style="font-family:verdana,sans-serif">I am also using Simbio and I usually run the leadfield calculation overnight since it takes approximatelly 12-15 hours for 64 EEG channels with a grid of 6 mm resolution ( 2.60 GHz, 32 GB RAM). <br></div><div class="gmail_default" style="font-family:verdana,sans-serif">I don't know whether there is a way to speed the process up. Maybe we just need to be patient, or work on a very powerful machine.<br><br></div><div class="gmail_default" style="font-family:verdana,sans-serif">Best,<br></div><div class="gmail_default" style="font-family:verdana,sans-serif">Debora<br></div><div class="gmail_default" style="font-family:verdana,sans-serif"><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 13, 2016 at 4:25 PM, Rajat Thomas <span dir="ltr"><<a href="mailto:r.thomas@nin.knaw.nl" target="_blank">r.thomas@nin.knaw.nl</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear all,<br>
<br>
Last week I asked for help with Simbio and after following the suggestion of volume reslicing magically the<br>
simbio based headmodel was created.<br>
<br>
But my leadfield calculations are taking way too long.<br>
It is a 128^3 grid and am running it on my desktop. (2.4 GHz, plenty of memory 32GB)<br>
<br>
Could anyone give me a rough ball park on how long it should take to create a leadfield?<br>
<br>
Thank you.<br>
Rajat<br>
<br>
<br>
<br>
Rajat Mani Thomas<br>
Social Brain Lab<br>
Netherlands Institute for Neuroscience<br>
Amsterdam<br>
<br>
________________________________________<br>
From: <a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a> <<a href="mailto:fieldtrip-bounces@science.ru.nl">fieldtrip-bounces@science.ru.nl</a>> on behalf of <a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a> <<a href="mailto:fieldtrip-request@science.ru.nl">fieldtrip-request@science.ru.nl</a>><br>
Sent: 08 April 2016 12:00<br>
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Subject: fieldtrip Digest, Vol 65, Issue 7<br>
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Today's Topics:<br>
<br>
1. Re: FEM using Simbio (Johannes Vorwerk)<br>
2. Re: FEM using Simbio (Cristiano Micheli)<br>
3. Dipole fitting (Giovanni Pellegrino)<br>
4. Birmingham-Illinois BRIDGE Fellowships (Ole Jensen)<br>
5. Using FieldTrip to analyse LFP recordings in rat<br>
(<a href="mailto:laetitia.lalla@inserm.fr">laetitia.lalla@inserm.fr</a>)<br>
<br>
<br>
----------------------------------------------------------------------<br>
<br>
Message: 1<br>
Date: Thu, 7 Apr 2016 14:25:42 +0200<br>
From: Johannes Vorwerk <<a href="mailto:j.vorwerk@uni-muenster.de">j.vorwerk@uni-muenster.de</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] FEM using Simbio<br>
Message-ID: <<a href="mailto:435735E3-7D87-4DD6-A2C1-E2BBFBBF4B44@googlemail.com">435735E3-7D87-4DD6-A2C1-E2BBFBBF4B44@googlemail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi,<br>
<br>
this question was already answered in this thread<br>
<br>
<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html</a> <<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html</a>><br>
<br>
If ft_volumereslice is not applied before the mesh generation, the afterwards applied transformation might flip the directions of the mesh, leading to the described error.<br>
<br>
Best,<br>
Johannes<br>
<br>
> Am 06.04.2016 um 16:03 schrieb Carsten Wolters <<a href="mailto:carsten.wolters@uni-muenster.de">carsten.wolters@uni-muenster.de</a>>:<br>
><br>
> Dear Rajat,<br>
><br>
> the element-node cards of SimBio-NeuroFEM need to follow certain orientations (see <a href="http://www.simbio.de" rel="noreferrer" target="_blank">www.simbio.de</a> <<a href="http://www.simbio.de/" rel="noreferrer" target="_blank">http://www.simbio.de/</a>>).<br>
><br>
> If you do not want to struggle with meshing/ordering, use the SimBio-VGRID mesher<br>
> <a href="http://vgrid.simbio.de/" rel="noreferrer" target="_blank">http://vgrid.simbio.de/</a> <<a href="http://vgrid.simbio.de/" rel="noreferrer" target="_blank">http://vgrid.simbio.de/</a>><br>
> that follows the required ordering of nodes. You might use this mesher to produce 1mm geometry-adapted FEM meshes<br>
> that show good overall performance, see<br>
> <a href="http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf" rel="noreferrer" target="_blank">http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf</a> <<a href="http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf" rel="noreferrer" target="_blank">http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf</a>><br>
> and<br>
> <a href="http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf" rel="noreferrer" target="_blank">http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf</a> <<a href="http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf" rel="noreferrer" target="_blank">http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf</a>><br>
> (latter was just accepted by NeuroImage).<br>
><br>
> Best regards<br>
> Carsten<br>
><br>
> Am 06.04.2016 um 15:10 schrieb Rajat Thomas:<br>
>> Dear all,<br>
>><br>
>> Has anyone used the FEM approach to Headmodels using Simbio recently?<br>
>><br>
>> If so, I get this error:<br>
>> "Elements have wrong orientation or are degenerated"<br>
>><br>
>> Any ideas?<br>
>><br>
>> cfg = [];<br>
>> cfg.method ='simbio';<br>
>> cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows mesh.tissyelabel<br>
>> vol = ft_prepare_headmodel(cfg, mesh);<br>
>><br>
>> And;<br>
>> ?<br>
>> disp(mesh)<br>
>> hex: [545883x8 double]<br>
>> pnt: [569722x3 double]<br>
>> labels: [545883x1 double]<br>
>> tissue: [545883x1 double]<br>
>> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}<br>
>> unit: 'mm'<br>
>> cfg: [1x1 struct]<br>
>><br>
>> Any help would be highly appreciated.<br>
>><br>
>> Rajat<br>
>><br>
>><br>
>><br>
>><br>
>><br>
>><br>
>> Rajat Mani Thomas<br>
>> Social Brain Lab<br>
>> Netherlands Institute for Neuroscience<br>
>> Amsterdam<br>
>><br>
>><br>
>> _______________________________________________<br>
>> fieldtrip mailing list<br>
>> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a> <mailto:<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
>> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a> <<a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a>><br>
> <carsten_wolters.vcf>_______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a> <mailto:<a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a>><br>
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<br>
Message: 2<br>
Date: Thu, 7 Apr 2016 17:36:37 +0200<br>
From: Cristiano Micheli <<a href="mailto:michelic72@gmail.com">michelic72@gmail.com</a>><br>
To: FieldTrip discussion list <<a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a>><br>
Subject: Re: [FieldTrip] FEM using Simbio<br>
Message-ID:<br>
<<a href="mailto:CADW7XCAQONsZ_ujPhkffskZ%2Bj-mnHnAzunS68CdKU6MLSosUPA@mail.gmail.com">CADW7XCAQONsZ_ujPhkffskZ+j-mnHnAzunS68CdKU6MLSosUPA@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Hi Rajat<br>
<br>
My guess is that the orientations of your hexahedrons are not correct.<br>
According to a low-level file's internal rules, elements' orientations have<br>
to abide strict rules (not sure what exactly the contraints are in this<br>
case though...).<br>
I had same problems when for example the triangular boundaries used to<br>
define the 3d hexahedral mesh were not topologically correct, to start with.<br>
Admittedly this approach requires a lot of technical expertise.<br>
Can I ask you what do you need a FEM model for?<br>
<br>
Regards<br>
Cris Micheli<br>
<br>
<br>
<br>
<br>
On Wed, Apr 6, 2016 at 3:10 PM, Rajat Thomas <<a href="mailto:r.thomas@nin.knaw.nl">r.thomas@nin.knaw.nl</a>> wrote:<br>
<br>
> Dear all,<br>
><br>
><br>
> Has anyone used the FEM approach to Headmodels using Simbio recently?<br>
><br>
><br>
> If so, I get this error:<br>
> "Elements have wrong orientation or are degenerated"<br>
><br>
> Any ideas?<br>
><br>
> cfg = [];<br>
><br>
> cfg.method ='simbio';<br>
><br>
> cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows<br>
> mesh.tissyelabel<br>
><br>
> vol = ft_prepare_headmodel(cfg, mesh);<br>
><br>
><br>
> And;<br>
><br>
> ?<br>
> disp(mesh)<br>
> hex: [545883x8 double]<br>
> pnt: [569722x3 double]<br>
> labels: [545883x1 double]<br>
> tissue: [545883x1 double]<br>
> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}<br>
> unit: 'mm'<br>
> cfg: [1x1 struct]<br>
><br>
><br>
> Any help would be highly appreciated.<br>
><br>
> Rajat<br>
><br>
><br>
><br>
><br>
><br>
><br>
> Rajat Mani Thomas<br>
> Social Brain Lab<br>
> Netherlands Institute for Neuroscience<br>
> Amsterdam<br>
><br>
> _______________________________________________<br>
> fieldtrip mailing list<br>
> <a href="mailto:fieldtrip@donders.ru.nl">fieldtrip@donders.ru.nl</a><br>
> <a href="http://mailman.science.ru.nl/mailman/listinfo/fieldtrip" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/mailman/listinfo/fieldtrip</a><br>
><br>
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<br>
Message: 3<br>
Date: Thu, 7 Apr 2016 15:02:05 -0400<br>
From: Giovanni Pellegrino <<a href="mailto:giovannipellegrino@gmail.com">giovannipellegrino@gmail.com</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Dipole fitting<br>
Message-ID:<br>
<CAN6FyLVw=e7gOOvGDo47fT3j0frr8FUAEcsm55O8ZzqA=<a href="mailto:u8GDw@mail.gmail.com">u8GDw@mail.gmail.com</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
Dear Fieldtrippers,<br>
<br>
Do you know if the FieldTrip Dipole Fitting has been compared to the CTF,<br>
Elekta, BESA or Curry? Are you aware of any study on this topic?<br>
<br>
Thanks in advance for your help<br>
<br>
Giovanni<br>
<br>
--<br>
Giovanni Pellegrino, MD<br>
Multimodal Functional Imaging Laboratory<br>
Montreal Neurological Institute, McGill University<br>
Address: 332 Duff Medical Building, 3775 rue University, Montreal, QC, H3A<br>
2B4, Canada<br>
Phone: (514) 398?1678<br>
Fax: (514) 398?7461<br>
Email: <a href="mailto:giovannipellegrino@gmail.com">giovannipellegrino@gmail.com</a>, <a href="mailto:giovanni.pellegrino2@mcgill.ca">giovanni.pellegrino2@mcgill.ca</a><br>
Homepage: <a href="http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleGiovanni" rel="noreferrer" target="_blank">http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleGiovanni</a><br>
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<br>
Message: 4<br>
Date: Fri, 8 Apr 2016 09:23:46 +0200<br>
From: Ole Jensen <<a href="mailto:ole.jensen@donders.ru.nl">ole.jensen@donders.ru.nl</a>><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Birmingham-Illinois BRIDGE Fellowships<br>
Message-ID: <<a href="mailto:57075C82.8030309@donders.ru.nl">57075C82.8030309@donders.ru.nl</a>><br>
Content-Type: text/plain; charset=utf-8; format=flowed<br>
<br>
Dear all,<br>
<br>
I would like to point you to a set of Birmingham-Illinois BRIDGE<br>
Fellowships providing some exciting research and career prospects:<br>
<a href="http://www.birminghamillinoisbridge.org/index.php/fellows/" rel="noreferrer" target="_blank">http://www.birminghamillinoisbridge.org/index.php/fellows/</a><br>
<br>
In particular the areas 'Cognition and Ageing' and 'Brain Trauma' could<br>
be relevant for candidates with EEG/MEG expertise.<br>
<br>
All the best,<br>
<br>
Ole<br>
<br>
--<br>
Prof. dr. Ole Jensen<br>
<a href="http://www.neuosc.com" rel="noreferrer" target="_blank">http://www.neuosc.com</a><br>
<br>
<br>
<br>
------------------------------<br>
<br>
Message: 5<br>
Date: Fri, 08 Apr 2016 10:27:58 +0200<br>
From: <a href="mailto:laetitia.lalla@inserm.fr">laetitia.lalla@inserm.fr</a><br>
To: <a href="mailto:fieldtrip@science.ru.nl">fieldtrip@science.ru.nl</a><br>
Subject: [FieldTrip] Using FieldTrip to analyse LFP recordings in rat<br>
Message-ID: <<a href="mailto:628babdc107aebd4cc7588ea87ce5ea6@inserm.fr">628babdc107aebd4cc7588ea87ce5ea6@inserm.fr</a>><br>
Content-Type: text/plain; charset="utf-8"<br>
<br>
<br>
<br>
Hello everyone,<br>
<br>
my name is Laetitia and I'm a Phd student in Marseille (France). I'm<br>
doing in-vivo recording in freely-moving rats : I implant them with 2<br>
electrodes deep into 2 different regions of the brain. I'm studying the<br>
Local Field Potentials and I want to use FieldTrip to analyse the data.<br>
<br>
To simplify :<br>
<br>
- I have 2 rats.<br>
<br>
- Each rat did 20 sessions of the task (on 20 different days).<br>
<br>
- Each session consists of 20 trials of condition 1 and 20 trials of<br>
condition 2.<br>
<br>
I have 2 questions.<br>
<br>
1) I have the feeling it would be meaningless to do "source<br>
reconstruction" because my electrodes are already deep inside my<br>
"source" and the LFP I am recording is very local. (My electrodes have<br>
32 channels separated by 20-200 ?m. The LFP is very very similar across<br>
all the channels, so I averaged over the 32 channels to have one signal<br>
for each region.)<br>
<br>
However, I see that 2 different functions exist for the statistics :<br>
FT_FREQSTATISTICS AND FT_SOURCESTATISTICS. So far, I've been using<br>
ft_freqstatistics but I encounter some issues (for exemple, doing<br>
monte-carlo permutation test to assess the imaginary coherence). I<br>
thought of computing it manually, but I'm thinking that maybe more stuff<br>
are implemented in ft_sourcestatisctics ?<br>
<br>
? Are these 2 functions fundamentally different or do they call the same<br>
sub-fonctions (and my problem has actually nothing to do with that) ?<br>
<br>
2) I'm a bit confused with the vocabulary from EEG and MEG studies (I'm<br>
not used to it yet...). From what I understood, in human studies, you<br>
can do comparison for a single subject (across trials) or across<br>
subjects. But I have 3 levels of comparisons in my design :<br>
<br>
- WITHIN A SESSION, I WANT TO COMPARE ACROSS TRIALS (the 20 trials of<br>
condition 1 VS the 20 trials of condition 2).<br>
<br>
- WITHIN A RAT, I WANT TO COMPARE ACROSS SESSIONS (between the 2<br>
conditions)<br>
<br>
- then - in the very end - ACROSS RATS. But I have only 2 rats so far,<br>
so I will deal with this later.<br>
<br>
I'm a bit confused when reading the tutorials and the mailing list,<br>
especially when it comes to the statistics... For example : this is from<br>
an email from 2013 by Eric Maris about "Nonparametric statistical<br>
testing of phase coherence"<br>
(<a href="http://mailman.science.ru.nl/pipermail/fieldtrip/2013-April/006401.html" rel="noreferrer" target="_blank">http://mailman.science.ru.nl/pipermail/fieldtrip/2013-April/006401.html</a>)<br>
"To compare coherence between conditions across subjects (instead of<br>
trials), you need a different statfun: depsamplesT (for a<br>
within-subjects design; subjects have participated in all conditions) or<br>
indepsamplesT (for a between-subjects design; subjects have participated<br>
in only one condition)."<br>
<br>
? If I want to compare across sessions (for a same rat), can I actually<br>
consider that my different sessions are "subjects"? And then compare<br>
coherence "across subjects" would be doing it "across sessions" ? And I<br>
would be in a "within-subject design" since my sessions involve the 2<br>
conditions every time ?<br>
<br>
I realise that it may be very confusing... I hope you will understand my<br>
problem !<br>
<br>
And if anyone already applied fieldtrip functions to do statistics on a<br>
different framework that the usual EEG/MEG, please let me know !<br>
<br>
Thanks a lot,<br>
<br>
Laetitia Lalla<br>
<br>
PhD Student in Neuroscience<br>
<br>
INMED, Marseille, France<br>
<br>
<br>
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</blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div><div><div><div><div><div><font face="verdana,sans-serif"><br>Debora Desideri</font><font face="verdana,sans-serif">, PhD Student<br></font></div></div><font face="verdana,sans-serif">BNP Lab - Neurology Department<br></font></div><font face="verdana,sans-serif">University Hospital Tübingen<br></font></div><font face="verdana,sans-serif">Eberhard Karls University Tübingen<br></font></div><font face="verdana,sans-serif">Hoppe-Seyler Str. 3<br></font></div><font face="verdana,sans-serif">D-72076 Tübingen<br></font></div><font face="verdana,sans-serif">Tel: +49 7071/29 80478<br></font><div><div><div><font face="verdana,sans-serif"><br></font></div></div></div></div></div></div></div>
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