[FieldTrip] Simbio works with ft_volumereslice but leadfield
Debora Desideri
deb.desideri at gmail.com
Fri Apr 15 09:55:43 CEST 2016
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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>> 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
>
> _______________________________________________
> 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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