[FieldTrip] Simbio works with ft_volumereslice but leadfield
Debora Desideri
deb.desideri at gmail.com
Sun Apr 17 21:08:32 CEST 2016
Dear Johannes,
yes, the calculation of the transfer matrix is actually the part that takes
so long (ft_prepare_vol_sens). But as you point out, it is maybe just a not
efficient matlab implementation...
Best,
Debora
On Sun, Apr 17, 2016 at 3:34 PM, Johannes Vorwerk <j.vorwerk at uni-muenster.de
> wrote:
> Hi,
>
> could you check if it’s the calculation of the transfer matrix
> (ft_prepare_vol_sens), which you can recoginze since the #electrode many
> equations are solved, or the call of leadfield_simbio that takes up the
> most time?
>
> It is normal that the matlab-code takes more time than the
> SimBio-standalon binary, since it includes some loops. I’ve never
> experienced such long computations as you did in my testings, so I didn’t
> think about it very much so far. One might try to find a way to formulate
> these parts without loops or use parallel loops at some points.
>
> Best,
> Johannes
>
> Am 15.04.2016 um 01:55 schrieb Debora Desideri <deb.desideri at gmail.com>:
>
> Dear Johannes,
> the time consuming part is when I call ft_prepare_leadfield. The I used
> this precomputed leadfields for the computation of the dipole solution and
> this is actually quite fast.
> I started to use the FEM model only recently and I thought the long
> lasting calculation was normal. Is there a way to have a faster
> compuatation of leadfields?
>
> Best,
> Debora
>
>
> On Thu, Apr 14, 2016 at 11:28 PM, Johannes Vorwerk <
> j.vorwerk at uni-muenster.de> wrote:
>
>> Hi Debora,
>>
>> could you indicate which part of the computation is the most time
>> consuming, i.e., calculation of the transfer matrix or the subsequent
>> computation of the dipole solutions? Principally, it should be possible to
>> parallelize many of these steps, however, this wasn’t added to the
>> checked-in code yet for reasons of stability/compatibility.
>>
>> Best,
>> Johannes
>>
>> Am 14.04.2016 um 02:21 schrieb Debora Desideri <deb.desideri at gmail.com>:
>>
>> 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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>>> When replying, please edit your Subject line so it is more specific
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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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>>>
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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
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>>
>>
>> _______________________________________________
>> fieldtrip mailing list
>> fieldtrip at donders.ru.nl
>> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>>
>
>
>
> --
>
> 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
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
>
>
> _______________________________________________
> fieldtrip mailing list
> fieldtrip at donders.ru.nl
> http://mailman.science.ru.nl/mailman/listinfo/fieldtrip
>
--
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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