[FieldTrip] 'dipoli' headmodel Windows version

Mon Sep 16 16:41:53 CEST 2024

Hi all,

FYI I just pushed some changes to the codebase (directly available on the master branch of the github repo), which should allow for the use of the dipole executable in windows.
We need to sort out a glitch with the automatic release mechanism before the functionality will also be available on the release branch (and consequently on the tagged release zip files). Please feel free to try it out: I only have limited windows computing resources available at my end, so it would be good to hear about other users’ experiences.

Looking forward to the balsamic vinegar and with best wishes,

Jan-Mathijs

On 13 Sep 2024, at 15:48, IRENE INCERTI <196344 at studenti.unimore.it> wrote:

You don't often get email from 196344 at studenti.unimore.it. Learn why this is important<https://aka.ms/LearnAboutSenderIdentification>

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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Ffieldtrip%2Ffieldtrip%2Fissues%2F1130&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147191073%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=7elggExVdGQTgTnfLqzdpgblScodvs0KSbt2uufQvk8%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<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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nilab.unimore.it%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fwpM7YrTGisYdiw0SxOGQ%2FUlDBGGxE6EMzawX6BEx7E%3D&reserved=0>

Via Campi, 287 - 41125 Modena (MO) ITALY
Mailto: irene.incerti at unimore.it<mailto:f.raimondi at unimore.it>
_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=SSggEjFMrMZhnILwFSd5tcVm0oE%2FnjnNEBrw5fCC%2FME%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=DfZPOlKLN7y6%2FJ3%2FGtMlQpApzXlfdT%2FSgW%2F3syfj1hM%3D&reserved=0>

_______________________________________________
fieldtrip mailing list
https://mailman.science.ru.nl/mailman/listinfo/fieldtrip<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmailman.science.ru.nl%2Fmailman%2Flistinfo%2Ffieldtrip&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=SSggEjFMrMZhnILwFSd5tcVm0oE%2FnjnNEBrw5fCC%2FME%3D&reserved=0>
https://doi.org/10.1371/journal.pcbi.1002202<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fdoi.org%2F10.1371%2Fjournal.pcbi.1002202&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=DfZPOlKLN7y6%2FJ3%2FGtMlQpApzXlfdT%2FSgW%2F3syfj1hM%3D&reserved=0>

--
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://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.nilab.unimore.it%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C2fe5d3a6bab8470ff88108dcd65db4b0%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638620945147347339%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C0%7C%7C%7C&sdata=fwpM7YrTGisYdiw0SxOGQ%2FUlDBGGxE6EMzawX6BEx7E%3D&reserved=0>

Via Campi, 287 - 41125 Modena (MO) ITALY
Mailto: irene.incerti at unimore.it<mailto:f.raimondi at unimore.it>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.science.ru.nl/pipermail/fieldtrip/attachments/20240916/a215f1ba/attachment.htm>