[FieldTrip] fieldtrip Digest, Vol 166, Issue 8
Richards, John
RICHARDS at mailbox.sc.edu
Sat Sep 14 13:57:28 CEST 2024
FYI, I run the dipoli and the bemcp on Linux; do these routinely to compare to FEM models. Even have a paper comparing the dipoli results to FEM results: Conte, S., & Richards, J.E. (2021). The influence of the head model conductor on the source localization of auditory evoked potentials. Brain Topography, 10.1007/s10548-021-00871-z
I would be glad to give advice. My use of it is fairly straightforward re the Fieldtrip call, though the scripts in which I use it are not straightforward.
John
***********************************************
John E. Richards
Carolina Distinguished Professor
Department of Psychology
University of South Carolina
Columbia, SC 29208
Dept Phone: 803 777 2079
Fax: 803 777 9558
Email: richards-john at sc.edu
https://jerlab.sc.edu/
***********************************************
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Today's Topics:
1. Re: 'dipoli' headmodel Linux version (IRENE INCERTI)
2. Re: 'dipoli' headmodel Linux version
(Schoffelen, J.M. (Jan Mathijs))
----------------------------------------------------------------------
Message: 1
Date: Fri, 13 Sep 2024 15:48:29 +0200
From: IRENE INCERTI <196344 at studenti.unimore.it>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] 'dipoli' headmodel Linux version
Message-ID:
<CAGyKoByYBFZ-2094=Amk0RMjxHdQsJUmHUQCyonJ9qGqDyEPBg at mail.gmail.com>
Content-Type: text/plain; charset="utf-8"
*Dear JM,*
I am pleased that you have attempted to use the dipoli executable. I was also able to open and run the executable; however, it prompts me to insert the 'filename1' but returns an 'out of memory' error and then, it crushes.
Do you think this issue could be related to the file's size or its extension? Could you please provide the dimensions and extension of your input file?
Additionally, how do you input the conductivities? Should they be entered immediately after the file name?
Thank you very much.
Il giorno gio 12 set 2024 alle ore 17:31 Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl> ha scritto:
> Hi Irene,
>
> As you may have noticed: the dipoli executable (dipoli.exe) cannot yet
> be directly accessed from within FieldTrip, in the same way as the
> other executables can be accessed (on the other operating systems). It
> shouldn't be altogether too difficult to get this up and running (in
> fact: I quickly tried this on one of the windows systems in the
> building, and was successful), and it surprises me a bit that nobody
> has ever made the effort to go the extra few steps that are needed. Or
> perhaps people have done this, but have never shared it. For a crate
> of nice vintage balsamico vinegar I would be up for the challenge. The
> way forward here would be to reopen this issue:
> https://gith/
> ub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1130&data=05%7C02%7CRICHARDS
> %40mailbox.sc.edu%7Cc9148d5458564f27c82008dcd4a44c66%7C4b2a4b19d135420
> e8bb2b1cd238998cc%7C0%7C0%7C638619049389942507%7CUnknown%7CTWFpbGZsb3d
> 8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C
> 0%7C%7C%7C&sdata=WyXO2WGqcBJIYrm3V42R1glRa2I7uJntUpF0NPG92OM%3D&reserv
> ed=0
> <https://git/
> hub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1130&data=05%7C02%7CRICHARD
> S%40mailbox.sc.edu%7Cc9148d5458564f27c82008dcd4a44c66%7C4b2a4b19d13542
> 0e8bb2b1cd238998cc%7C0%7C0%7C638619049389948643%7CUnknown%7CTWFpbGZsb3
> d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=Zwi%2BHzfysLpT0FE9mrvqg1tcBpfAHvMUPXY0VdNmQl4%3D&reserved=0> and take it from there. I wouldn't mind to create a PR on github with code changes that builds in support for dipoli in windows, provided this is considered to be a good overall improvement, and provided that other people write the documentation, and do the testing.
>
> Best wishes,
> JM
>
>
>
>
> On 12 Sep 2024, at 10:29, IRENE INCERTI via fieldtrip <
> fieldtrip at science.ru.nl> wrote:
>
> Dear Fieldtrippers,
> I am a new user of FieldTrip.
>
> I'm working with a Windows system.
> I'm currently attempting to perform an EEG source reconstruction with
> realistic head geometries. FieldTrip implements the Boundary Element
> Method
> (BEM) for EEG using the foreward ft_compute_leadfield function.
> However, this requires that an EEG BEM model will be built with
> ft_prepare_model function, where in the cfg.method field, you must
> specify 'dipoli', 'bemcp', or 'openmeg'. Initially, as I was working
> with a Windows machine, I tried using 'bemcp'. Unfortunately, the head
> model failed because, starting from 6000 vertices (3000 for the brain,
> 2000 for the skull, and
> 1000 for the scalp), it produced a 1000x6000 double conductivity
> matrix. I have also read in other discussion list that 'bemcp' may
> encounter issues and, in some cases, does not compute at all. I would
> like to try using 'dipoli', command-line executable or Linux version.
>
> Does anyone have experience with this method? Could you please explain
> how it works and what input is required?
>
> Thank you very much for your assistance.
>
> Best regards,
> Irene
>
> --
> *Irene Incerti, PhD student*
>
> *UNI**MORE* University of Modena and Reggio Emilia *Department of
> Biomedical, Metabolic, and Neural Sciences* Center for Neuroscience
> and Neurotechnologies *Neuromorphic Intelligence LABoratory*
> https://www/.
> nilab.unimore.it%2F&data=05%7C02%7CRICHARDS%40mailbox.sc.edu%7Cc9148d5
> 458564f27c82008dcd4a44c66%7C4b2a4b19d135420e8bb2b1cd238998cc%7C0%7C0%7
> C638619049389953178%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIj
> oiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=nHigsIeO58
> d%2FOw7hDk6W0Cienz8Oa8RcH3FhdlApEDk%3D&reserved=0
> <https://www/
> .nilab.unimore.it%2F&data=05%7C02%7CRICHARDS%40mailbox.sc.edu%7Cc9148d
> 5458564f27c82008dcd4a44c66%7C4b2a4b19d135420e8bb2b1cd238998cc%7C0%7C0%
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> 8UgCvcJShfuYY8QsaM7Lq5nin9zm1iaYIs%3D&reserved=0>
>
> Via Campi, 287 - 41125 Modena (MO) ITALY
> Mailto: irene.incerti at unimore.it <f.raimondi at unimore.it>
> _______________________________________________
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>
--
*Irene Incerti, PhD student*
*UNI**MORE* University of Modena and Reggio Emilia
*Department of Biomedical, Metabolic, and Neural Sciences* Center for Neuroscience and Neurotechnologies *Neuromorphic Intelligence LABoratory*
https://www.nilab.unimore.it/
Via Campi, 287 - 41125 Modena (MO) ITALY
Mailto: irene.incerti at unimore.it <f.raimondi at unimore.it>
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Message: 2
Date: Fri, 13 Sep 2024 14:29:16 +0000
From: "Schoffelen, J.M. (Jan Mathijs)"
<janmathijs.schoffelen at donders.ru.nl>
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Subject: Re: [FieldTrip] 'dipoli' headmodel Linux version
Message-ID: <7BC06ADA-CC68-4E26-8CCE-479433E21003 at donders.ru.nl>
Content-Type: text/plain; charset="utf-8"
Hi Irene,
If you type dipoli.exe -h on the windows command line, you will see the documentation about how the executable can be used. In combination with the code in ft_headmodel_dipoli (which basically is a 'gateway' into the executable, and it writes the boundaries into a set of files that the executable can work with) I think you might be able to get up and running.
Nonetheless, on the long run I think that we should go the extra mile, and make a principled implementation, so that people don't have to reinvent the wheel over and over.
Best wishes,
Jan-Mathijs
On 13 Sep 2024, at 15:48, IRENE INCERTI <196344 at studenti.unimore.it> wrote:
Dear JM,
I am pleased that you have attempted to use the dipoli executable. I was also able to open and run the executable; however, it prompts me to insert the 'filename1' but returns an 'out of memory' error and then, it crushes. Do you think this issue could be related to the file's size or its extension? Could you please provide the dimensions and extension of your input file?
Additionally, how do you input the conductivities? Should they be entered immediately after the file name?
Thank you very much.
Il giorno gio 12 set 2024 alle ore 17:31 Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> ha scritto:
Hi Irene,
As you may have noticed: the dipoli executable (dipoli.exe) cannot yet be directly accessed from within FieldTrip, in the same way as the other executables can be accessed (on the other operating systems). It shouldn't be altogether too difficult to get this up and running (in fact: I quickly tried this on one of the windows systems in the building, and was successful), and it surprises me a bit that nobody has ever made the effort to go the extra few steps that are needed. Or perhaps people have done this, but have never shared it. For a crate of nice vintage balsamico vinegar I would be up for the challenge. The way forward here would be to reopen this issue: https://github.com/fieldtrip/fieldtrip/issues/1130<https://github.com/fieldtrip/fieldtrip/issues/1130> and take it from there. I wouldn't mind to create a PR on github with code changes that builds in support for dipoli in windows, provided this is considered to be a good overall improvement, and provided that other people write the documentation, and do the testing.
Best wishes,
JM
On 12 Sep 2024, at 10:29, IRENE INCERTI via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:
Dear Fieldtrippers,
I am a new user of FieldTrip.
I'm working with a Windows system.
I'm currently attempting to perform an EEG source reconstruction with realistic head geometries. FieldTrip implements the Boundary Element Method (BEM) for EEG using the foreward ft_compute_leadfield function. However, this requires that an EEG BEM model will be built with ft_prepare_model function, where in the cfg.method field, you must specify 'dipoli', 'bemcp', or 'openmeg'. Initially, as I was working with a Windows machine, I tried using 'bemcp'. Unfortunately, the head model failed because, starting from 6000 vertices (3000 for the brain, 2000 for the skull, and 1000 for the scalp), it produced a 1000x6000 double conductivity matrix. I have also read in other discussion list that 'bemcp' may encounter issues and, in some cases, does not compute at all. I would like to try using 'dipoli', command-line executable or Linux version.
Does anyone have experience with this method? Could you please explain how it works and what input is required?
Thank you very much for your assistance.
Best regards,
Irene
--
Irene Incerti, PhD student
UNIMORE University of Modena and Reggio Emilia Department of Biomedical, Metabolic, and Neural Sciences Center for Neuroscience and Neurotechnologies Neuromorphic Intelligence LABoratory https://www.nilab.unimore.it/<https://www.nilab.unimore.it/>
Via Campi, 287 - 41125 Modena (MO) ITALY
Mailto: irene.incerti at unimore.it<mailto:f.raimondi at unimore.it>
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https://doi.org/10.1371/journal.pcbi.1002202<https://doi.org/10.1371/journal.pcbi.1002202>
--
Irene Incerti, PhD student
UNIMORE University of Modena and Reggio Emilia Department of Biomedical, Metabolic, and Neural Sciences Center for Neuroscience and Neurotechnologies Neuromorphic Intelligence LABoratory https://www.nilab.unimore.it/<https://www.nilab.unimore.it/>
Via Campi, 287 - 41125 Modena (MO) ITALY
Mailto: irene.incerti at unimore.it<mailto:f.raimondi at unimore.it>
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