[FieldTrip] Electrode localization stl file

Stout, Megan stout at wustl.edu
Thu Dec 19 16:56:05 CET 2024 

Hello,

Just wanted to follow up on this.

Best,

Megan Stout
Clinical Research Assistant II
Department of Neurology
Washington University School of Medicine



________________________________
From: Stout, Megan <stout at wustl.edu>
Sent: Friday, December 13, 2024 2:42 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Cc: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl>
Subject: Re: [FieldTrip] Electrode localization stl file

I was afraid that might be the case. Is there a way to save the electrode positions separately in different file format? How would I do that if I would like to eventually co-register them with an MRI?


Best,

Megan Stout
Clinical Research Assistant II
Department of Neurology
Washington University School of Medicine



________________________________
From: fieldtrip <fieldtrip-bounces at science.ru.nl> on behalf of Schoffelen, J.M. (Jan Mathijs) via fieldtrip <fieldtrip at science.ru.nl>
Sent: Friday, December 13, 2024 12:59 PM
To: FieldTrip discussion list <fieldtrip at science.ru.nl>
Cc: Schoffelen, J.M. (Jan Mathijs) <janmathijs.schoffelen at donders.ru.nl>
Subject: Re: [FieldTrip] Electrode localization stl file


* External Email - Caution *

Hi Megan,

Thanks for the clarification. I am not sure about this, but I don’t think that an stl-file without triangulation information exists. In other words: what you wish to achieve cannot be done with the stl file-format.

Best wishes,
Jan-Mathijs


On 13 Dec 2024, at 15:16, Stout, Megan via fieldtrip <fieldtrip at science.ru.nl> wrote:

Hello Jan-Mathijs,

There are two main reasons why I am trying to save the headshape with electrodes as an stl file:

  1.
I would like to co-register and/or compare the electrode localization done with FT on a 3D scan with electrode localization done via Geodesic Photogrammetry System to compare the accuracy
  2.
An added benefit of being able to display the 3D image with electrodes in presentations

We are eventually wanting to co-register MRI and EEG, but want to make sure our electrode localization is accurate.

Best,

Megan Stout
Clinical Research Assistant II
Department of Neurology
Washington University School of Medicine



________________________________
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Sent: Thursday, December 12, 2024 5:00 AM
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Today's Topics:

   1. Electrode localization stl file (Stout, Megan)
   2. Re: Electrode localization stl file
      (Schoffelen, J.M. (Jan Mathijs))


----------------------------------------------------------------------

Message: 1
Date: Wed, 11 Dec 2024 22:00:31 +0000
From: "Stout, Megan" <stout at wustl.edu<mailto:stout at wustl.edu>>
To: "fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>" <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: [FieldTrip] Electrode localization stl file
Message-ID:
        <BY5PR02MB6770AE76B5AD306398CEE61DA08C2 at BY5PR02MB6770.namprd02.prod.outlook.com<mailto:BY5PR02MB6770AE76B5AD306398CEE61DA08C2 at BY5PR02MB6770.namprd02.prod.outlook.com>>

Content-Type: text/plain; charset="iso-8859-1"

Hello Fieldtrippers!

*I am new to matlab so please excuse any ignorance!

I am using fieldtrip for electrode localization on a 3D scan, following the Localizing Electrodes Using a 3D Scanner<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Felectrode%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C8699e07249d246144b5e08dd2045ae2f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638702208049056588%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C20000%7C%7C%7C&sdata=EH3siEHTMUudoEsqnJ4JxK9n6fnRPGh70%2BUdgfv6LeA%3D&reserved=0<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Felectrode%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C8699e07249d246144b5e08dd2045ae2f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638702208049070582%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C20000%7C%7C%7C&sdata=SgrDoi4Ap9JvKQ0ZudSKIvlKDIAWwESet4%2BTTdr0qkw%3D&reserved=0>> tutorial and I end up with a .fig file of the 3D head with the electrodes, but I need an .stl or .obj file. I used ft_write_headshape to convert to stl (which just uses matlab's stlwrite), but it will only convert the headshape mesh without the electrodes. I am not entirely sure of the issue, but I believe it may have something to do with the fact that the electrodes do not have their own triangulation (tri), just the pos, and both tri and pos are required for stlwrite in this case. I have attached the code below. Can anyone help me figure out how to get the headshape with electrodes converted into an stl or obj file?

Code for localizing electrodes (using tutorial above):

>> headshape = ft_read_headshape("C:\Users\stout\Downloads\testfile\testfile.obj")
>> headshape = ft_convert_units(headshape, 'mm');
>> ft_plot_headshape(headshape)

>> cfg = [];
cfg.method = 'interactive';
headshape = ft_meshrealign(cfg, headshape);
>> ft_plot_headshape(headshape, 'axes', true)

>> cfg = [];
cfg.method = 'headshape';
cfg.channel = {'nas', 'lpa', 'rpa'};
fiducials = ft_electrodeplacement(cfg, headshape);

>> cfg = [];
cfg.method        = 'fiducial';
cfg.coordsys      = 'ctf';
cfg.fiducial.nas  = fiducials.elecpos(1,:); %position of NAS
cfg.fiducial.lpa  = fiducials.elecpos(2,:); %position of LPA
cfg.fiducial.rpa  = fiducials.elecpos(3,:); %position of RPA
headshape = ft_meshrealign(cfg, headshape);

>> ft_plot_mesh(headshape, 'axes', true)
>> cfg = [];
cfg.method = 'headshape';
elec = ft_electrodeplacement(cfg, headshape);

>> ft_plot_headshape(headshape)
ft_plot_sens(elec, 'label', 'on', 'fontsize', 15, 'elecshape', 'disc', 'elecsize', 10)


%Subsequent code for converting to stl:

>> ft_write_headshape('testelec.stl', elec, 'format', 'stl')
Unrecognized field name "tri".

Error in ft_write_headshape (line 194)
    stlwrite(filename, mesh.tri, mesh.pos);
                       ^^^^^^^^

>> ft_write_headshape('test.stl', headshape, 'format', 'stl')
Wrote 939812 facets




Best,

Megan Stout
Clinical Research Assistant II
Department of Neurology
Washington University School of Medicine



________________________________
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Message: 2
Date: Thu, 12 Dec 2024 07:48:58 +0000
From: "Schoffelen, J.M. (Jan Mathijs)"
        <janmathijs.schoffelen at donders.ru.nl<mailto:janmathijs.schoffelen at donders.ru.nl>>
To: FieldTrip discussion list <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>>
Subject: Re: [FieldTrip] Electrode localization stl file
Message-ID: <72CEC4D3-1C25-4F7C-93A4-BABFC27CA6E2 at donders.ru.nl<mailto:72CEC4D3-1C25-4F7C-93A4-BABFC27CA6E2 at donders.ru.nl>>
Content-Type: text/plain; charset="utf-8"

Dear Megan,

Could you elaborate on your expectations/the requirement that the electrodes can be saved into an *.stl file? Is there external software that needs electrodes in in stl format?

Practically, ft_write_headshape is typically used to write a headshape mesh into a file, where indeed the expectation is that the object to-be-written (at least when the requested dataformat is .stl) contains both a set of points/vertices, and a description of a surface (triangles). The electrode definition is an object that indeed only contains points, and no triangles.

Best wishes,
Jan-Mathijs






On 11 Dec 2024, at 23:00, Stout, Megan via fieldtrip <fieldtrip at science.ru.nl<mailto:fieldtrip at science.ru.nl>> wrote:

Hello Fieldtrippers!

*I am new to matlab so please excuse any ignorance!

I am using fieldtrip for electrode localization on a 3D scan, following the Localizing Electrodes Using a 3D Scanner<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Felectrode%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C8699e07249d246144b5e08dd2045ae2f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638702208049111544%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C20000%7C%7C%7C&sdata=peyL9QlJbsoTA2kN2yvxJzdRIxlmvEKoTqVIt6hBPHM%3D&reserved=0<https://eur01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwww.fieldtriptoolbox.org%2Ftutorial%2Felectrode%2F&data=05%7C02%7Cfieldtrip%40science.ru.nl%7C8699e07249d246144b5e08dd2045ae2f%7C084578d9400d4a5aa7c7e76ca47af400%7C1%7C0%7C638702208049125068%7CUnknown%7CTWFpbGZsb3d8eyJFbXB0eU1hcGkiOnRydWUsIlYiOiIwLjAuMDAwMCIsIlAiOiJXaW4zMiIsIkFOIjoiTWFpbCIsIldUIjoyfQ%3D%3D%7C20000%7C%7C%7C&sdata=6oNipOnHNWISIAq%2FBN14YGgOhiguuXJGr5MnI0kldfc%3D&reserved=0>> tutorial and I end up with a .fig file of the 3D head with the electrodes, but I need an .stl or .obj file. I used ft_write_headshape to convert to stl (which just uses matlab's stlwrite), but it will only convert the headshape mesh without the electrodes. I am not entirely sure of the issue, but I believe it may have something to do with the fact that the electrodes do not have their own triangulation (tri), just the pos, and both tri and pos are required for stlwrite in this case. I have attached the code below. Can anyone help me figure out how to get the headshape with electrodes converted into an stl or obj file?

Code for localizing electrodes (using tutorial above):

>> headshape = ft_read_headshape("C:\Users\stout\Downloads\testfile\testfile.obj")
>> headshape = ft_convert_units(headshape, 'mm');
>> ft_plot_headshape(headshape)

>> cfg = [];
cfg.method = 'interactive';
headshape = ft_meshrealign(cfg, headshape);
>> ft_plot_headshape(headshape, 'axes', true)

>> cfg = [];
cfg.method = 'headshape';
cfg.channel = {'nas', 'lpa', 'rpa'};
fiducials = ft_electrodeplacement(cfg, headshape);

>> cfg = [];
cfg.method        = 'fiducial';
cfg.coordsys      = 'ctf';
cfg.fiducial.nas  = fiducials.elecpos(1,:); %position of NAS
cfg.fiducial.lpa  = fiducials.elecpos(2,:); %position of LPA
cfg.fiducial.rpa  = fiducials.elecpos(3,:); %position of RPA
headshape = ft_meshrealign(cfg, headshape);

>> ft_plot_mesh(headshape, 'axes', true)
>> cfg = [];
cfg.method = 'headshape';
elec = ft_electrodeplacement(cfg, headshape);

>> ft_plot_headshape(headshape)
ft_plot_sens(elec, 'label', 'on', 'fontsize', 15, 'elecshape', 'disc', 'elecsize', 10)


%Subsequent code for converting to stl:

>> ft_write_headshape('testelec.stl', elec, 'format', 'stl')
Unrecognized field name "tri".

Error in ft_write_headshape (line 194)
    stlwrite(filename, mesh.tri, mesh.pos);
                       ^^^^^^^^

>> ft_write_headshape('test.stl', headshape, 'format', 'stl')
Wrote 939812 facets




Best,

Megan Stout
Clinical Research Assistant II
Department of Neurology
Washington University School of Medicine




________________________________
The materials in this message are private and may contain Protected Healthcare Information or other information of a sensitive nature. If you are not the intended recipient, be advised that any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited. If you have received this email in error, please immediately notify the sender via telephone or return mail.
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End of fieldtrip Digest, Vol 169, Issue 2
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