[FieldTrip] Simbio works with ft_volumereslice but leadfield

Debora Desideri deb.desideri at gmail.com
Thu Apr 14 10:21:08 CEST 2016


Dear Rajat,
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).
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.

Best,
Debora


On Wed, Apr 13, 2016 at 4:25 PM, Rajat Thomas <r.thomas at nin.knaw.nl> wrote:

> 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
>
> ________________________________________
> From: fieldtrip-bounces at science.ru.nl <fieldtrip-bounces at science.ru.nl>
> on behalf of fieldtrip-request at science.ru.nl <
> fieldtrip-request at science.ru.nl>
> Sent: 08 April 2016 12:00
> To: fieldtrip at science.ru.nl
> Subject: fieldtrip Digest, Vol 65, Issue 7
>
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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
> >>
> >>
> >> _______________________________________________
> >> fieldtrip mailing list
> >> fieldtrip at donders.ru.nl <mailto:fieldtrip at donders.ru.nl>
> >> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip <
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip>
> > <carsten_wolters.vcf>_______________________________________________
> > fieldtrip mailing list
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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>
> Content-Type: text/plain; charset="utf-8"
>
> 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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-- 

Debora Desideri, PhD Student
BNP Lab - Neurology Department
University Hospital Tübingen
Eberhard Karls University Tübingen
Hoppe-Seyler Str. 3
D-72076 Tübingen
Tel: +49 7071/29 80478
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