[FieldTrip] Simbio works with ft_volumereslice but leadfield
Rajat Thomas
r.thomas at nin.knaw.nl
Wed Apr 13 16:25:51 CEST 2016
Dear all,
Last week I asked for help with Simbio and after following the suggestion of volume reslicing magically the
simbio based headmodel was created.
But my leadfield calculations are taking way too long.
It is a 128^3 grid and am running it on my desktop. (2.4 GHz, plenty of memory 32GB)
Could anyone give me a rough ball park on how long it should take to create a leadfield?
Thank you.
Rajat
Rajat Mani Thomas
Social Brain Lab
Netherlands Institute for Neuroscience
Amsterdam
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Today's Topics:
1. Re: FEM using Simbio (Johannes Vorwerk)
2. Re: FEM using Simbio (Cristiano Micheli)
3. Dipole fitting (Giovanni Pellegrino)
4. Birmingham-Illinois BRIDGE Fellowships (Ole Jensen)
5. Using FieldTrip to analyse LFP recordings in rat
(laetitia.lalla at inserm.fr)
----------------------------------------------------------------------
Message: 1
Date: Thu, 7 Apr 2016 14:25:42 +0200
From: Johannes Vorwerk <j.vorwerk at uni-muenster.de>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] FEM using Simbio
Message-ID: <435735E3-7D87-4DD6-A2C1-E2BBFBBF4B44 at googlemail.com>
Content-Type: text/plain; charset="utf-8"
Hi,
this question was already answered in this thread
http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html <http://mailman.science.ru.nl/pipermail/fieldtrip/2016-March/010274.html>
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.
Best,
Johannes
> Am 06.04.2016 um 16:03 schrieb Carsten Wolters <carsten.wolters at uni-muenster.de>:
>
> Dear Rajat,
>
> the element-node cards of SimBio-NeuroFEM need to follow certain orientations (see www.simbio.de <http://www.simbio.de/>).
>
> If you do not want to struggle with meshing/ordering, use the SimBio-VGRID mesher
> http://vgrid.simbio.de/ <http://vgrid.simbio.de/>
> that follows the required ordering of nodes. You might use this mesher to produce 1mm geometry-adapted FEM meshes
> that show good overall performance, see
> http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf <http://www.sci.utah.edu/~wolters/PaperWolters/2007/WoltersEtAl_IEEE_TBME_2007.pdf>
> and
> http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf <http://www.sci.utah.edu/~wolters/PaperWolters/2016/WagnerLuckaVorwerkHerrmannNolteBurgerWolters_NeuroImage_2016.pdf>
> (latter was just accepted by NeuroImage).
>
> Best regards
> Carsten
>
> Am 06.04.2016 um 15:10 schrieb Rajat Thomas:
>> Dear all,
>>
>> Has anyone used the FEM approach to Headmodels using Simbio recently?
>>
>> If so, I get this error:
>> "Elements have wrong orientation or are degenerated"
>>
>> Any ideas?
>>
>> cfg = [];
>> cfg.method ='simbio';
>> cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows mesh.tissyelabel
>> vol = ft_prepare_headmodel(cfg, mesh);
>>
>> And;
>> ?
>> disp(mesh)
>> hex: [545883x8 double]
>> pnt: [569722x3 double]
>> labels: [545883x1 double]
>> tissue: [545883x1 double]
>> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}
>> unit: 'mm'
>> cfg: [1x1 struct]
>>
>> Any help would be highly appreciated.
>>
>> Rajat
>>
>>
>>
>>
>>
>>
>> Rajat Mani Thomas
>> Social Brain Lab
>> Netherlands Institute for Neuroscience
>> Amsterdam
>>
>>
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Message: 2
Date: Thu, 7 Apr 2016 17:36:37 +0200
From: Cristiano Micheli <michelic72 at gmail.com>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] FEM using Simbio
Message-ID:
<CADW7XCAQONsZ_ujPhkffskZ+j-mnHnAzunS68CdKU6MLSosUPA at mail.gmail.com>
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Hi Rajat
My guess is that the orientations of your hexahedrons are not correct.
According to a low-level file's internal rules, elements' orientations have
to abide strict rules (not sure what exactly the contraints are in this
case though...).
I had same problems when for example the triangular boundaries used to
define the 3d hexahedral mesh were not topologically correct, to start with.
Admittedly this approach requires a lot of technical expertise.
Can I ask you what do you need a FEM model for?
Regards
Cris Micheli
On Wed, Apr 6, 2016 at 3:10 PM, Rajat Thomas <r.thomas at nin.knaw.nl> wrote:
> Dear all,
>
>
> Has anyone used the FEM approach to Headmodels using Simbio recently?
>
>
> If so, I get this error:
> "Elements have wrong orientation or are degenerated"
>
> Any ideas?
>
> cfg = [];
>
> cfg.method ='simbio';
>
> cfg.conductivity = [0.33 0.14 1.79 0.01 0.43]; % order follows
> mesh.tissyelabel
>
> vol = ft_prepare_headmodel(cfg, mesh);
>
>
> And;
>
> ?
> disp(mesh)
> hex: [545883x8 double]
> pnt: [569722x3 double]
> labels: [545883x1 double]
> tissue: [545883x1 double]
> tissuelabel: {'csf' 'gray' 'scalp' 'skull' 'white'}
> unit: 'mm'
> cfg: [1x1 struct]
>
>
> Any help would be highly appreciated.
>
> Rajat
>
>
>
>
>
>
> Rajat Mani Thomas
> Social Brain Lab
> Netherlands Institute for Neuroscience
> Amsterdam
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
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Message: 3
Date: Thu, 7 Apr 2016 15:02:05 -0400
From: Giovanni Pellegrino <giovannipellegrino at gmail.com>
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Dipole fitting
Message-ID:
<CAN6FyLVw=e7gOOvGDo47fT3j0frr8FUAEcsm55O8ZzqA=u8GDw at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
Dear Fieldtrippers,
Do you know if the FieldTrip Dipole Fitting has been compared to the CTF,
Elekta, BESA or Curry? Are you aware of any study on this topic?
Thanks in advance for your help
Giovanni
--
Giovanni Pellegrino, MD
Multimodal Functional Imaging Laboratory
Montreal Neurological Institute, McGill University
Address: 332 Duff Medical Building, 3775 rue University, Montreal, QC, H3A
2B4, Canada
Phone: (514) 398?1678
Fax: (514) 398?7461
Email: giovannipellegrino at gmail.com, giovanni.pellegrino2 at mcgill.ca
Homepage: http://www.bic.mni.mcgill.ca/ResearchLabsMFIL/PeopleGiovanni
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Message: 4
Date: Fri, 8 Apr 2016 09:23:46 +0200
From: Ole Jensen <ole.jensen at donders.ru.nl>
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Birmingham-Illinois BRIDGE Fellowships
Message-ID: <57075C82.8030309 at donders.ru.nl>
Content-Type: text/plain; charset=utf-8; format=flowed
Dear all,
I would like to point you to a set of Birmingham-Illinois BRIDGE
Fellowships providing some exciting research and career prospects:
http://www.birminghamillinoisbridge.org/index.php/fellows/
In particular the areas 'Cognition and Ageing' and 'Brain Trauma' could
be relevant for candidates with EEG/MEG expertise.
All the best,
Ole
--
Prof. dr. Ole Jensen
http://www.neuosc.com
------------------------------
Message: 5
Date: Fri, 08 Apr 2016 10:27:58 +0200
From: laetitia.lalla at inserm.fr
To: fieldtrip at science.ru.nl
Subject: [FieldTrip] Using FieldTrip to analyse LFP recordings in rat
Message-ID: <628babdc107aebd4cc7588ea87ce5ea6 at inserm.fr>
Content-Type: text/plain; charset="utf-8"
Hello everyone,
my name is Laetitia and I'm a Phd student in Marseille (France). I'm
doing in-vivo recording in freely-moving rats : I implant them with 2
electrodes deep into 2 different regions of the brain. I'm studying the
Local Field Potentials and I want to use FieldTrip to analyse the data.
To simplify :
- I have 2 rats.
- Each rat did 20 sessions of the task (on 20 different days).
- Each session consists of 20 trials of condition 1 and 20 trials of
condition 2.
I have 2 questions.
1) I have the feeling it would be meaningless to do "source
reconstruction" because my electrodes are already deep inside my
"source" and the LFP I am recording is very local. (My electrodes have
32 channels separated by 20-200 ?m. The LFP is very very similar across
all the channels, so I averaged over the 32 channels to have one signal
for each region.)
However, I see that 2 different functions exist for the statistics :
FT_FREQSTATISTICS AND FT_SOURCESTATISTICS. So far, I've been using
ft_freqstatistics but I encounter some issues (for exemple, doing
monte-carlo permutation test to assess the imaginary coherence). I
thought of computing it manually, but I'm thinking that maybe more stuff
are implemented in ft_sourcestatisctics ?
? Are these 2 functions fundamentally different or do they call the same
sub-fonctions (and my problem has actually nothing to do with that) ?
2) I'm a bit confused with the vocabulary from EEG and MEG studies (I'm
not used to it yet...). From what I understood, in human studies, you
can do comparison for a single subject (across trials) or across
subjects. But I have 3 levels of comparisons in my design :
- WITHIN A SESSION, I WANT TO COMPARE ACROSS TRIALS (the 20 trials of
condition 1 VS the 20 trials of condition 2).
- WITHIN A RAT, I WANT TO COMPARE ACROSS SESSIONS (between the 2
conditions)
- then - in the very end - ACROSS RATS. But I have only 2 rats so far,
so I will deal with this later.
I'm a bit confused when reading the tutorials and the mailing list,
especially when it comes to the statistics... For example : this is from
an email from 2013 by Eric Maris about "Nonparametric statistical
testing of phase coherence"
(http://mailman.science.ru.nl/pipermail/fieldtrip/2013-April/006401.html)
"To compare coherence between conditions across subjects (instead of
trials), you need a different statfun: depsamplesT (for a
within-subjects design; subjects have participated in all conditions) or
indepsamplesT (for a between-subjects design; subjects have participated
in only one condition)."
? If I want to compare across sessions (for a same rat), can I actually
consider that my different sessions are "subjects"? And then compare
coherence "across subjects" would be doing it "across sessions" ? And I
would be in a "within-subject design" since my sessions involve the 2
conditions every time ?
I realise that it may be very confusing... I hope you will understand my
problem !
And if anyone already applied fieldtrip functions to do statistics on a
different framework that the usual EEG/MEG, please let me know !
Thanks a lot,
Laetitia Lalla
PhD Student in Neuroscience
INMED, Marseille, France
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