From oupu at dtu.dk  Wed Dec  2 10:29:25 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Wed, 2 Dec 2020 09:29:25 +0000
Subject: [Simnibs-discuss] tDCS optimisation
In-Reply-To: <LO2P265MB1167591D3F7634636C8E0D86CAF60@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>
References: <LO2P265MB1167591D3F7634636C8E0D86CAF60@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <02aa250dafe74c7d89a3e414fc8c6ba1@dtu.dk>

Hi Harry,


This could be related to the shell.

Can you try to start a terminal, then write bash and open matlab from there?


Hopefully the paths are then set correctly.


Best,

Oula




________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Harry Corker <hc888 at bath.ac.uk>
Sent: Sunday, November 29, 2020 5:36:48 PM
To: discuss at simnibs.org
Subject: [Simnibs-discuss] tDCS optimisation

Dear reader,

I am an undergrad researcher at university investigating tDCS and am enjoying learning with your simnibs software. I am currently trying to create a leadfield for tDCS optimisation but run into this error...
[cid:c70b3f86-c9d5-424c-904f-285cbb560e31]
The matlab file is saved in the ernie folder and I haven't edited the code. Any help would be much appreciated.

Kind regards,

Harry

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From oupu at dtu.dk  Wed Dec  2 10:33:46 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Wed, 2 Dec 2020 09:33:46 +0000
Subject: [Simnibs-discuss] About the usage of custom CAT12 segmentation
In-Reply-To: <HK2PR03MB425889BA4FC797A0778AAC0FB8F90@HK2PR03MB4258.apcprd03.prod.outlook.com>
References: <HK2PR03MB425889BA4FC797A0778AAC0FB8F90@HK2PR03MB4258.apcprd03.prod.outlook.com>
Message-ID: <c4b195b157b84faeb60b5fed856f7895@dtu.dk>

Hi Ti Chun Hang Eden,


I haven't tried the stroke tool, so not sure what it outputs, but if the stroke lesion is segmented out separately you could assign that to CSF in the mask_prep folder (after binarization).


In the final mesh the lesioned area would then be CSF, but you can afterwards relabel it back to stroke lesion using the segmentation mask if you want.


Best,
Oula


________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of TI, Chun Hang Eden <1155138422 at link.cuhk.edu.hk>
Sent: Thursday, November 26, 2020 2:14:14 AM
To: simnibs-discuss at drcmr.dk
Subject: [Simnibs-discuss] About the usage of custom CAT12 segmentation

Dear Sir/Madam,

I have been using SIMNIBS headreco segmentation to generate cortical surface reconstruction for stroke patients, knowing CAT12 is not optimized for these types of brains.

The newest version of CAT12 includes a function (Stroke Lesion Correction), which produces a better segmentation result after my inspection. Is there a way to incorporate these segmentation results directly, to proceed to the next stage?

 I tried to use the segmentation results from that, to replace the results in /segments/cat directories, and binarized the segmentation mask. However, when I run the preparecat function, I encounter the following errors.
[cid:df45b0e2-26fb-4b88-a9b2-6d60ad27ee85]

I suspect that the error results from the difference of the number of vertices of the mesh generated from the initial preparevol command and the custom segmentation results from new CAT12.
Is there any way to generate a .off file based on the new CAT12 features?

I have been using Simnibs for a long time and really appreciate your team's effort in maintaining and updating the software for better progression of this research field. Look forward to your reply

Best regards,

Ti Chun Hang Eden
PhD, Department of Biomedical Engineering
The Chinese University of Hong Kong
Email: 1155138422 at link.cuhk.edu.hk
Mobile: +852 91339153
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From utkarshpancholi6387 at gmail.com  Wed Dec  9 11:47:08 2020
From: utkarshpancholi6387 at gmail.com (Utkarsh Pancholi)
Date: Wed, 9 Dec 2020 16:17:08 +0530
Subject: [Simnibs-discuss] Error occurs during matlab simulation for .nii
	files
Message-ID: <CAFvJZmgTWTE7GxFbcvZHyzyyVBogkogwtFgjGn_G2Zeh-fQMUQ@mail.gmail.com>

  Sir,

Hope you are doing well.

Sir I have accessed the MRI database from
https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME.

I have processed that .nii file from one Alzheimer's patient in SimNIBS
using command Headreco all but MATLAB is showing errors.

Can you please tell me how i can get the correct images for processing in
SIMNIBS

What should I consider before image selection ?

Please let me know. Thank you. Regards

-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI
ASSISTANT PROFESSOR
BIOMEDICAL ENGINEERING
L.D COLLEGE OF ENGINEERING
AHMEDABAD-380015
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From desmond.oathes at gmail.com  Wed Dec  9 16:45:35 2020
From: desmond.oathes at gmail.com (Desmond Oathes)
Date: Wed, 9 Dec 2020 10:45:35 -0500
Subject: [Simnibs-discuss] mri2mesh error
Message-ID: <CAFCmLD=ZDbbyxGD_vV7eBpZ2O7X8TE9SkFqJP2x6eutD_pMcFw@mail.gmail.com>

Hi there,

I'm having the same error as:

https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html

But I'm running Mojave 10.14.6 Mac OSX.

Per the instructions here:

https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000052.html

I tried:

gmsh m2m_P124/tmp/subcortical_FS.stl

And it looks like a closed surface.

Thanks in advance for any advice,
Desmond
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From Nathan.Smyk at Pennmedicine.upenn.edu  Wed Dec  9 17:27:56 2020
From: Nathan.Smyk at Pennmedicine.upenn.edu (Smyk, Nathan)
Date: Wed, 9 Dec 2020 16:27:56 +0000
Subject: [Simnibs-discuss] mri2mesh error
Message-ID: <BL0PR04MB49475CACD2499D9A38EC5875C1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>

Good morning Valerie,

This is a long shot e-mail! My name is Nate Smyk, and I'm working at the University of Pennsylvania in neuroimaging, and I am having the same issue with Simnibs that you had reported here: https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html. I saw Axel responded saying Mac Catalina might be the issue (which I am also running on now). Did you happen to find a fix for this fseek issue? Any insight would be GREATLY appreciated!!!

ERROR- fseek
/Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335
failed.exiting mri2mesh after error


Best,
Nate Smyk
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From axelt at drcmr.dk  Wed Dec  9 17:37:28 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Wed, 9 Dec 2020 17:37:28 +0100
Subject: [Simnibs-discuss] mri2mesh error
In-Reply-To: <BL0PR04MB49475CACD2499D9A38EC5875C1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>
References: <BL0PR04MB49475CACD2499D9A38EC5875C1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>
Message-ID: <5859b753-34a5-eb0c-774d-494bfdd9734f@drcmr.dk>

Hi,

we tracked the error down to the use of Freesurfer 7 instead of 
Freesurfer 6.

mri2mesh uses mris_convert from freesurfer to convert the the freesurfer 
surfaces to .stl-files. Up to version 6, mris_convert wrote ascii 
.stl-files; since freesurfer 7, it writes only binary .stl-files. 
Because meshfix can only read ascii stl-files, it crashes.

So, for now, the work around is to use Freesurfer 6.0.1...

Hope this helps.

Best regards,

Axel



On 12/9/2020 5:27 PM, Smyk, Nathan wrote:
>
> Good morning Valerie,
>
> This is a long shot e-mail! My name is Nate Smyk, and I?m working at 
> the University of Pennsylvania in neuroimaging, and I am having the 
> same issue with Simnibs that you had reported here: 
> https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html 
> <https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html>. 
> I saw Axel responded saying Mac Catalina might be the issue (which I 
> am also running on now). Did you happen to find a fix for this fseek 
> issue? Any insight would be GREATLY appreciated!!!
>
> ERROR- fseek
>
> /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335
>
> failed.exiting mri2mesh after error
>
> Best,
>
> Nate Smyk
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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From desmond.oathes at gmail.com  Wed Dec  9 17:53:03 2020
From: desmond.oathes at gmail.com (Desmond Oathes)
Date: Wed, 9 Dec 2020 11:53:03 -0500
Subject: [Simnibs-discuss] mri2mesh error
In-Reply-To: <5859b753-34a5-eb0c-774d-494bfdd9734f@drcmr.dk>
References: <BL0PR04MB49475CACD2499D9A38EC5875C1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>
 <5859b753-34a5-eb0c-774d-494bfdd9734f@drcmr.dk>
Message-ID: <CAFCmLDn6r2-daTjdWG5umawid=k=qmLNHhWrTTW_D4CZ07616Q@mail.gmail.com>

Will give it a try.  Thanks much!

On Wed, Dec 9, 2020, 11:37 AM Axel Thielscher <axelt at drcmr.dk> wrote:

> Hi,
>
> we tracked the error down to the use of Freesurfer 7 instead of Freesurfer
> 6.
>
> mri2mesh uses mris_convert from freesurfer to convert the the freesurfer
> surfaces to .stl-files. Up to version 6, mris_convert wrote ascii
> .stl-files; since freesurfer 7, it writes only binary .stl-files. Because
> meshfix can only read ascii stl-files, it crashes.
>
> So, for now, the work around is to use Freesurfer 6.0.1...
>
> Hope this helps.
>
> Best regards,
>
> Axel
>
>
>
> On 12/9/2020 5:27 PM, Smyk, Nathan wrote:
>
> Good morning Valerie,
>
>
>
> This is a long shot e-mail! My name is Nate Smyk, and I?m working at the
> University of Pennsylvania in neuroimaging, and I am having the same issue
> with Simnibs that you had reported here:
> https://mailman.drcmr.dk/pipermail/simnibs-discuss/2020-May/000051.html.
> I saw Axel responded saying Mac Catalina might be the issue (which I am
> also running on now). Did you happen to find a fix for this fseek issue?
> Any insight would be GREATLY appreciated!!!
>
>
>
> ERROR- fseek
>
>
> /Users/guilherme/simnibs_supporting/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335
>
> failed.exiting mri2mesh after error
>
>
>
>
>
> Best,
>
> Nate Smyk
>
> _______________________________________________
> Simnibs-discuss mailing listSimnibs-discuss at drcmr.dkhttps://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
> --
> Dr. Axel Thielscher
> Associate Professor
> Danish Research Center for Magnetic Resonance
> Copenhagen University Hospital Hvidovre
> DK-2650 Hvidovre, Denmarkwww.drcmr.dk
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngbyhttp://www.healthtech.dtu.dk/
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From inesviolante at gmail.com  Wed Dec  9 18:40:42 2020
From: inesviolante at gmail.com (=?Windows-1252?Q?In=EAs_Violante?=)
Date: Wed, 9 Dec 2020 17:40:42 +0000
Subject: [Simnibs-discuss] hippocampal segmentation to stl
Message-ID: <LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>

Hello,

I?ve just tried headreco and it is really cool.
I would like to have a segmentation of the hippocampus in the same space as the meshes generated by headreco.
I have the hippocampus segmentation from freesurfer aligned to the subject space. This is a .nii.gz file

How can I now convert this to stl and have it in  the same space as the other meshes generated by headreco?

Thank you in advance!

All the best,

ines

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From oupu at dtu.dk  Thu Dec 10 07:53:39 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Thu, 10 Dec 2020 06:53:39 +0000
Subject: [Simnibs-discuss] Error occurs during matlab simulation for
	.nii files
In-Reply-To: <CAFvJZmgTWTE7GxFbcvZHyzyyVBogkogwtFgjGn_G2Zeh-fQMUQ@mail.gmail.com>
References: <CAFvJZmgTWTE7GxFbcvZHyzyyVBogkogwtFgjGn_G2Zeh-fQMUQ@mail.gmail.com>
Message-ID: <4f2c21d7812d4812b009e5b028b92d56@dtu.dk>

Hi Utkarsh,


When you run headreco there should be a headreco_log.html file that is produced.


Could you send that to us?


Thanks!


Best,

Oula

________________________________
From: Utkarsh Pancholi <utkarshpancholi6387 at gmail.com>
Sent: Wednesday, December 9, 2020 11:47:08 AM
To: discuss at simnibs.org; support at simnibs.org
Subject: Error occurs during matlab simulation for .nii files

  Sir,

Hope you are doing well.

Sir I have accessed the MRI database from https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME.

I have processed that .nii file from one Alzheimer's patient in SimNIBS using command Headreco all but MATLAB is showing errors.

Can you please tell me how i can get the correct images for processing in SIMNIBS

What should I consider before image selection ?

Please let me know. Thank you. Regards

-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI
ASSISTANT PROFESSOR
BIOMEDICAL ENGINEERING
L.D COLLEGE OF ENGINEERING
AHMEDABAD-380015
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From Nathan.Smyk at Pennmedicine.upenn.edu  Wed Dec  9 17:38:43 2020
From: Nathan.Smyk at Pennmedicine.upenn.edu (Smyk, Nathan)
Date: Wed, 9 Dec 2020 16:38:43 +0000
Subject: [Simnibs-discuss] [External] Re:  mri2mesh error
In-Reply-To: <5859b753-34a5-eb0c-774d-494bfdd9734f@drcmr.dk>
References: <BL0PR04MB49475CACD2499D9A38EC5875C1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>,
 <5859b753-34a5-eb0c-774d-494bfdd9734f@drcmr.dk>
Message-ID: <BL0PR04MB49479C13CB47A9CA32575AFBC1CC0@BL0PR04MB4947.namprd04.prod.outlook.com>

Thanks so much! This is great info; I'll try this. I appreciate it!

Best,
Nate Smyk
________________________________
From: Axel Thielscher <axelt at drcmr.dk>
Sent: Wednesday, December 9, 2020 11:37 AM
To: Smyk, Nathan <Nathan.Smyk at Pennmedicine.upenn.edu>; mrsnicolson at gmail.com <mrsnicolson at gmail.com>
Cc: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>
Subject: [External] Re: [Simnibs-discuss] mri2mesh error


Hi,

we tracked the error down to the use of Freesurfer 7 instead of Freesurfer 6.

mri2mesh uses mris_convert from freesurfer to convert the the freesurfer surfaces to .stl-files. Up to version 6, mris_convert wrote ascii .stl-files; since freesurfer 7, it writes only binary .stl-files. Because meshfix can only read ascii stl-files, it crashes.

So, for now, the work around is to use Freesurfer 6.0.1...

Hope this helps.

Best regards,

Axel




On 12/9/2020 5:27 PM, Smyk, Nathan wrote:
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From oupu at dtu.dk  Fri Dec 11 08:38:39 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Fri, 11 Dec 2020 07:38:39 +0000
Subject: [Simnibs-discuss] Error occurs during matlab simulation for
	.nii files
In-Reply-To: <CAFvJZmhn1CUE3UzBtkh7uFx6Z0TFWRWGT578rrzOwgWwRwa62g@mail.gmail.com>
References: <CAFvJZmgTWTE7GxFbcvZHyzyyVBogkogwtFgjGn_G2Zeh-fQMUQ@mail.gmail.com>
 <4f2c21d7812d4812b009e5b028b92d56@dtu.dk>,
 <CAFvJZmhn1CUE3UzBtkh7uFx6Z0TFWRWGT578rrzOwgWwRwa62g@mail.gmail.com>
Message-ID: <684de86e2ee043bcbd90ee77eb22cfd3@dtu.dk>

Try running without the "--cat" flag. The --cat option is default in simnibs 3.2.


If you specifically do not want to use CAT12 you should include a "--no-cat" flag.

________________________________
From: Utkarsh Pancholi <utkarshpancholi6387 at gmail.com>
Sent: Thursday, December 10, 2020 9:44:21 AM
To: Oula Puonti
Cc: discuss at simnibs.org; support at simnibs.org
Subject: Re: Error occurs during matlab simulation for .nii files

Sure, here it is.
-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI
ASSISTANT PROFESSOR
BIOMEDICAL ENGINEERING
L.D COLLEGE OF ENGINEERING
AHMEDABAD-380015


On Thu, Dec 10, 2020 at 12:23 PM Oula Puonti <oupu at dtu.dk<mailto:oupu at dtu.dk>> wrote:

Hi Utkarsh,


When you run headreco there should be a headreco_log.html file that is produced.


Could you send that to us?


Thanks!


Best,

Oula

________________________________
From: Utkarsh Pancholi <utkarshpancholi6387 at gmail.com<mailto:utkarshpancholi6387 at gmail.com>>
Sent: Wednesday, December 9, 2020 11:47:08 AM
To: discuss at simnibs.org<mailto:discuss at simnibs.org>; support at simnibs.org<mailto:support at simnibs.org>
Subject: Error occurs during matlab simulation for .nii files

  Sir,

Hope you are doing well.

Sir I have accessed the MRI database from https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME.

I have processed that .nii file from one Alzheimer's patient in SimNIBS using command Headreco all but MATLAB is showing errors.

Can you please tell me how i can get the correct images for processing in SIMNIBS

What should I consider before image selection ?

Please let me know. Thank you. Regards

-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI
ASSISTANT PROFESSOR
BIOMEDICAL ENGINEERING
L.D COLLEGE OF ENGINEERING
AHMEDABAD-380015
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From axelt at drcmr.dk  Fri Dec 11 21:39:43 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Fri, 11 Dec 2020 21:39:43 +0100
Subject: [Simnibs-discuss] hippocampal segmentation to stl
In-Reply-To: <LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>
References: <LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>
Message-ID: <15b7a94e-0407-9f4f-a574-d2bb47b06e75@drcmr.dk>

Hi Ines,

when you open the nifti-file in freeview, is it then coregistered with 
the <subid>_T1fs_conform.nii.gz which headreco creates? If not, you can 
first run freesurfer and use the T1 and T2 which freesurfer stores as 
input to headreco.

You can then try the nii2msh tool, which puts the data from niftis into 
the mesh.

Let us know in case you get stuck.

Best regards,

Axel


On 12/9/2020 6:40 PM, In?s Violante wrote:
>
> Hello,
>
> I?ve just tried headreco and it is really cool.
>
> I would like to have a segmentation of the hippocampus in the same 
> space as the meshes generated by headreco.
>
> I have the hippocampus segmentation from freesurfer aligned to the 
> subject space. This is a .nii.gz file
>
> How can I now convert this to stl and have it in? the same space as 
> the other meshes generated by headreco?
>
> Thank you in advance!
>
> All the best,
>
> ines
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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From utkarshpancholi6387 at gmail.com  Thu Dec 10 09:44:21 2020
From: utkarshpancholi6387 at gmail.com (Utkarsh Pancholi)
Date: Thu, 10 Dec 2020 14:14:21 +0530
Subject: [Simnibs-discuss] Error occurs during matlab simulation for
	.nii files
In-Reply-To: <4f2c21d7812d4812b009e5b028b92d56@dtu.dk>
References: <CAFvJZmgTWTE7GxFbcvZHyzyyVBogkogwtFgjGn_G2Zeh-fQMUQ@mail.gmail.com>
 <4f2c21d7812d4812b009e5b028b92d56@dtu.dk>
Message-ID: <CAFvJZmhn1CUE3UzBtkh7uFx6Z0TFWRWGT578rrzOwgWwRwa62g@mail.gmail.com>

Sure, here it is.
-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI
ASSISTANT PROFESSOR
BIOMEDICAL ENGINEERING
L.D COLLEGE OF ENGINEERING
AHMEDABAD-380015


On Thu, Dec 10, 2020 at 12:23 PM Oula Puonti <oupu at dtu.dk> wrote:

> Hi Utkarsh,
>
>
> When you run headreco there should be a headreco_log.html file that is
> produced.
>
>
> Could you send that to us?
>
>
> Thanks!
>
>
> Best,
>
> Oula
> ------------------------------
> *From:* Utkarsh Pancholi <utkarshpancholi6387 at gmail.com>
> *Sent:* Wednesday, December 9, 2020 11:47:08 AM
> *To:* discuss at simnibs.org; support at simnibs.org
> *Subject:* Error occurs during matlab simulation for .nii files
>
>   Sir,
>
> Hope you are doing well.
>
> Sir I have accessed the MRI database from
> https://ida.loni.usc.edu/login.jsp?project=ADNI&page=HOME.
>
> I have processed that .nii file from one Alzheimer's patient in SimNIBS
> using command Headreco all but MATLAB is showing errors.
>
> Can you please tell me how i can get the correct images for processing in
> SIMNIBS
>
> What should I consider before image selection ?
>
> Please let me know. Thank you. Regards
>
>
> -----------------------------------------------------------------------------------------------------
> UTKARSH V. PANCHOLI
> ASSISTANT PROFESSOR
> BIOMEDICAL ENGINEERING
> L.D COLLEGE OF ENGINEERING
> AHMEDABAD-380015
>
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From inesviolante at gmail.com  Mon Dec 14 12:51:52 2020
From: inesviolante at gmail.com (=?Windows-1252?Q?In=EAs_Violante?=)
Date: Mon, 14 Dec 2020 11:51:52 +0000
Subject: [Simnibs-discuss] hippocampal segmentation to stl
In-Reply-To: <15b7a94e-0407-9f4f-a574-d2bb47b06e75@drcmr.dk>
References: <LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>,
 <15b7a94e-0407-9f4f-a574-d2bb47b06e75@drcmr.dk>
Message-ID: <LOYP123MB34077AE205CF4CF2FAF9344AAFC70@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>

Hi Axel,

Thanks for the quick reply.
I tried that but with no luck. See command line output below.


 nii2msh -ev TIDES_P2T_S1_FreeSf/TIDES_P2T_S1/mri/lHippocampus.nii.gz TIDES_P2T_S1.msh lHipp.msh



[ simnibs ]INFO: Creating tensor visualization

Traceback (most recent call last):

  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 92, in <module>

    main()

  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", line 71, in main

    aniso_tissues=[1, 2])

  File "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/simulation/cond.py", line 173, in cond2elmdata

    assert len(anisotropy_volume.shape) == 4

AssertionError


Could this be because the volume is smaller than the expected from the T1 mesh?

All the best,

Ines


--
Dr Ines Violante
Lecturer in Psychological Neuroscience
School of Psychology | Faculty of Health and Medical Sciences
Room 32 AC 04
University of Surrey | Guildford GU2 7XH



From: Axel Thielscher <axelt at drcmr.dk>
Date: Friday, 11 December 2020 at 20:39
To: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>, inesviolante at gmail.com <inesviolante at gmail.com>
Subject: Re: [Simnibs-discuss] hippocampal segmentation to stl

Hi Ines,

when you open the nifti-file in freeview, is it then coregistered with the <subid>_T1fs_conform.nii.gz which headreco creates? If not, you can first run freesurfer and use the T1 and T2 which freesurfer stores as input to headreco.

You can then try the nii2msh tool, which puts the data from niftis into the mesh.

Let us know in case you get stuck.

Best regards,

Axel


On 12/9/2020 6:40 PM, In?s Violante wrote:
Hello,

I?ve just tried headreco and it is really cool.
I would like to have a segmentation of the hippocampus in the same space as the meshes generated by headreco.
I have the hippocampus segmentation from freesurfer aligned to the subject space. This is a .nii.gz file

How can I now convert this to stl and have it in  the same space as the other meshes generated by headreco?

Thank you in advance!

All the best,

ines




_______________________________________________

Simnibs-discuss mailing list

Simnibs-discuss at drcmr.dk<mailto:Simnibs-discuss at drcmr.dk>

https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

--

Dr. Axel Thielscher

Associate Professor

Danish Research Center for Magnetic Resonance

Copenhagen University Hospital Hvidovre

DK-2650 Hvidovre, Denmark

www.drcmr.dk<http://www.drcmr.dk>

&

Department of Health Technology

Technical University of Denmark

DK-2800 Kgs. Lyngby

http://www.healthtech.dtu.dk/
-->
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From axelt at drcmr.dk  Mon Dec 14 19:17:24 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Mon, 14 Dec 2020 19:17:24 +0100
Subject: [Simnibs-discuss] hippocampal segmentation to stl
In-Reply-To: <LOYP123MB34077AE205CF4CF2FAF9344AAFC70@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>
References: <LOYP123MB34074B0EEC2FDB18E10734BDAFCC0@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>
 <15b7a94e-0407-9f4f-a574-d2bb47b06e75@drcmr.dk>
 <LOYP123MB34077AE205CF4CF2FAF9344AAFC70@LOYP123MB3407.GBRP123.PROD.OUTLOOK.COM>
Message-ID: <43a5e105-ad9e-84cc-20bd-ab873047141e@drcmr.dk>

Dear Ines,

the description in the simnibs documentation is not very clear, I am 
sorry for this. You can use nii2mesh -h to get a bit more information 
(not not much though). Please try calling it without the -ev.

Best regards,

Axel

On 12/14/2020 12:51 PM, In?s Violante wrote:
>
> Hi Axel,
>
> Thanks for the quick reply.
>
> I tried that but with no luck. See command line output below.
>
> nii2msh -ev TIDES_P2T_S1_FreeSf/TIDES_P2T_S1/mri/lHippocampus.nii.gz 
> TIDES_P2T_S1.msh lHipp.msh
>
> [ simnibs ]INFO: Creating tensor visualization
>
> Traceback (most recent call last):
>
> File 
> "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", 
> line 92, in <module>
>
> main()
>
> File 
> "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/nii2msh.py", 
> line 71, in main
>
> aniso_tissues=[1, 2])
>
> File 
> "/Users/ines/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/simulation/cond.py", 
> line 173, in cond2elmdata
>
> assert len(anisotropy_volume.shape) == 4
>
> AssertionError
>
> Could this be because the volume is smaller than the expected from the 
> T1 mesh?
>
> All the best,
>
> Ines
>
> --
>
> Dr Ines Violante
> Lecturer in Psychological Neuroscience
> School of Psychology | Faculty of Health and?Medical Sciences
> Room 32 AC 04
>
> University of Surrey | Guildford GU2 7XH
>
> *From: *Axel Thielscher <axelt at drcmr.dk>
> *Date: *Friday, 11 December 2020 at 20:39
> *To: *simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>, 
> inesviolante at gmail.com <inesviolante at gmail.com>
> *Subject: *Re: [Simnibs-discuss] hippocampal segmentation to stl
>
> Hi Ines,
>
> when you open the nifti-file in freeview, is it then coregistered with 
> the <subid>_T1fs_conform.nii.gz which headreco creates? If not, you 
> can first run freesurfer and use the T1 and T2 which freesurfer stores 
> as input to headreco.
>
> You can then try the nii2msh tool, which puts the data from niftis 
> into the mesh.
>
> Let us know in case you get stuck.
>
> Best regards,
>
> Axel
>
> On 12/9/2020 6:40 PM, In?s Violante wrote:
>
>     Hello,
>
>     I?ve just tried headreco and it is really cool.
>
>     I would like to have a segmentation of the hippocampus in the same
>     space as the meshes generated by headreco.
>
>     I have the hippocampus segmentation from freesurfer aligned to the
>     subject space. This is a .nii.gz file
>
>     How can I now convert this to stl and have it in? the same space
>     as the other meshes generated by headreco?
>
>     Thank you in advance!
>
>     All the best,
>
>     ines
>
>
>
>     _______________________________________________
>
>     Simnibs-discuss mailing list
>
>     Simnibs-discuss at drcmr.dk  <mailto:Simnibs-discuss at drcmr.dk>
>
>     https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss  <https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss>
>
> -- 
> Dr. Axel Thielscher
> Associate Professor
> Danish Research Center for Magnetic Resonance
> Copenhagen University Hospital Hvidovre
> DK-2650 Hvidovre, Denmark
> www.drcmr.dk  <http://www.drcmr.dk>
> &
> Department of Health Technology
> Technical University of Denmark
> DK-2800 Kgs. Lyngby
> http://www.healthtech.dtu.dk/  <http://www.healthtech.dtu.dk/>
>
> -->
>
-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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From 3231937959 at qq.com  Tue Dec 15 01:27:55 2020
From: 3231937959 at qq.com (=?gb18030?B?wfXPsL3c?=)
Date: Tue, 15 Dec 2020 08:27:55 +0800
Subject: [Simnibs-discuss] about using SIMNIBS
Message-ID: <tencent_B6F5A968933402B06F4616F1ABC646759A0A@qq.com>

SIMNIBS community,&nbsp;


I am a new user. I wished someone could help to answer the questions:
1) Can the electrodes be placed under the skull instead of on the scalp?
2) Can we design the customized coil shape? What tools will we design those customized coils?
3) Can we have customized electrode? Specify any location, except for the 10-20 position?
4) what is the tool we can import MRI raw data in DICOM format?



I appreiavte&nbsp;your helps. Thanks.


JS
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From lorenzo.fabbri at mavs.uta.edu  Tue Dec 15 17:51:28 2020
From: lorenzo.fabbri at mavs.uta.edu (Fabbri, Lorenzo)
Date: Tue, 15 Dec 2020 16:51:28 +0000
Subject: [Simnibs-discuss] Installation Issue
Message-ID: <SN6PR01MB4864462B524354B29A930382BAC60@SN6PR01MB4864.prod.exchangelabs.com>

Hi,

I have completed the SimNibs installation but when trying to generate the FEM mesh in Brainstorm, I get the following error:

SimNIBS is not installed or not added to the system path etc.

Is there a specific destination where the simnibs_env folder should be in?

Thank you for your help,

Lorenzo.


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From oupu at dtu.dk  Wed Dec 16 08:19:19 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Wed, 16 Dec 2020 07:19:19 +0000
Subject: [Simnibs-discuss] Installation Issue
In-Reply-To: <SN6PR01MB4864462B524354B29A930382BAC60@SN6PR01MB4864.prod.exchangelabs.com>
References: <SN6PR01MB4864462B524354B29A930382BAC60@SN6PR01MB4864.prod.exchangelabs.com>
Message-ID: <64702106a48b4728a1f075ec7bc4aa04@dtu.dk>

Hi Lorenzo,


Can you give a few more details, namely:


- Which operating system are you using?


- When you say "trying to generate the FEM mesh in Brainstorm" do you mean that you're trying to call SimNIBS through brainstorm?


It seems that the system path does not include SimNIBS. There's no specific location SimNIBS needs to be installed, but the system path needs to be updated so the installation can be found.


Best,

Oula


________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Fabbri, Lorenzo <lorenzo.fabbri at mavs.uta.edu>
Sent: Tuesday, December 15, 2020 5:51:28 PM
To: discuss at simnibs.org
Subject: [Simnibs-discuss] Installation Issue

Hi,

I have completed the SimNibs installation but when trying to generate the FEM mesh in Brainstorm, I get the following error:

SimNIBS is not installed or not added to the system path etc.

Is there a specific destination where the simnibs_env folder should be in?

Thank you for your help,

Lorenzo.


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From oupu at dtu.dk  Wed Dec 16 08:32:18 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Wed, 16 Dec 2020 07:32:18 +0000
Subject: [Simnibs-discuss] about using SIMNIBS
In-Reply-To: <tencent_B6F5A968933402B06F4616F1ABC646759A0A@qq.com>
References: <tencent_B6F5A968933402B06F4616F1ABC646759A0A@qq.com>
Message-ID: <a1072b80e3bf4ded9040a392b2306e35@dtu.dk>

Hi JS,


1) Simnibs expects the electrodes to be on the scalp. When you say under the skull, are you referring to intra-cranial electrodes?


2) Yes that's possible, see attached articles and a matlab script.


3) Yes, that's also possible. You can either use the GUI, see (https://simnibs.github.io/simnibs/build/html/tutorial/gui.html) or using matlab or python scripts, see (https://simnibs.github.io/simnibs/build/html/tutorial/scripting.html). Note in the scripts, the positions can be a coordinate as well, not just a position in an EEG cap.


4) I typically use the dcm2niix to convert dicoms to nifti, and the I can run simnibs on the nifti images. You can get dcm2niix from here:

https://github.com/rordenlab/dcm2niix


Best,

Oula



________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of ??? <3231937959 at qq.com>
Sent: Tuesday, December 15, 2020 1:27:55 AM
To: discuss
Subject: [Simnibs-discuss] about using SIMNIBS

SIMNIBS community,

I am a new user. I wished someone could help to answer the questions:
1) Can the electrodes be placed under the skull instead of on the scalp?
2) Can we design the customized coil shape? What tools will we design those customized coils?
3) Can we have customized electrode? Specify any location, except for the 10-20 position?
4) what is the tool we can import MRI raw data in DICOM format?

I appreiavte your helps. Thanks.

JS
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From fabio.masina83 at gmail.com  Thu Dec 17 08:57:41 2020
From: fabio.masina83 at gmail.com (Fabio Masina)
Date: Thu, 17 Dec 2020 08:57:41 +0100
Subject: [Simnibs-discuss] electric field estimation without individual MR
Message-ID: <CAPJmCpGn1nWbWr54tEOyOn3MVJPHCn2Hu2hXrPEK2A2NNZk1=g@mail.gmail.com>

 Dear colleagues,

I am writing a revision regarding NIBS and I am interested in the
comparison of the electric field derived from all the tDCS and TMS studies
I selected for this revision. So far, I have collected the basic
information will be important to run the electric field estimation with
SimNIBS, but I am wondering whether I can approximate the electric field
for each of these studies without having the individual magnetic resonance
of participants. Since in my review I would like to compare the electric
fields in a qualitative fashion, do you think it can be appropriate to
perform each estimation using the head model of the example dataset I found
here (https://simnibs.github.io/simnibs/build/html/dataset.html)?
Alternatively, can I run the estimation by using a template?

Thank you in advance for your interest in my question.

Best.


-- 

*Fabio Masina, PhD*

IRCCS, Ospedale San Camillo
Via Alberoni 70, 30126
Venice, Italy
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From fabio.masina83 at gmail.com  Thu Dec 17 09:02:09 2020
From: fabio.masina83 at gmail.com (Fabio Masina)
Date: Thu, 17 Dec 2020 09:02:09 +0100
Subject: [Simnibs-discuss] electric field estimation without individual MR
Message-ID: <CAPJmCpGQ2w9WyYvoD-Exghgd1TVugisiWGSfKML10tVVT9h-cg@mail.gmail.com>

 Dear colleagues,

I am writing a revision regarding NIBS and I am interested in the
comparison of the electric field derived from all the tDCS and TMS studies
I selected for this revision. So far, I have collected the basic
information will be important to run the electric field estimation with
SimNIBS, but I am wondering whether I can approximate the electric field
for each of these studies without having the individual magnetic resonance
of participants. Since in my review I would like to compare the electric
fields in a qualitative fashion, do you think it can be appropriate to
perform each estimation using the head model of the example dataset I found
here (https://simnibs.github.io/simnibs/build/html/dataset.html)?
Alternatively, can I run the estimation by using a template?

Thank you in advance for your interest in my question.

Best.


-- 

*Fabio Masina, PhD*

IRCCS, Ospedale San Camillo
Via Alberoni 70, 30126
Venice, Italy
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From 3231937959 at qq.com  Sat Dec 19 16:12:33 2020
From: 3231937959 at qq.com (=?gb18030?B?wfXPsL3c?=)
Date: Sat, 19 Dec 2020 23:12:33 +0800
Subject: [Simnibs-discuss] I wished to apply SIMNIBS when I put electrodes
	inside a skull.
Message-ID: <tencent_FB2DD829234DF83F63473AFFFACEB4371A09@qq.com>

Hi Oula and all SIMNIBS community,


Thank you for taking time to reply my last email.


1)&nbsp;When I say under the skull, I mean I wished put&nbsp; electrodes inside skull, or&nbsp;intra-cranial&nbsp;electrodes.&nbsp; We can reduce current if electrodes are put into skull.&nbsp;I hope I could compare their&nbsp; EF on the scalp vs inside skull.&nbsp;


2) I also wish to apply&nbsp; SIMNIBS for Deep brain stimulation (DBS) simulation. In this case, electrodes are also inside a skull.


If SIMNIBS does not allow electrodes sitting inside a skull, will you have a plan to update SIMNIBS to meet this new need? and When, if you will have the plan.&nbsp;&nbsp;If you will not do it, will you like to give me some suggestions so that I could follow your sugestion to update?


Your reply are great helps.&nbsp;


JS
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From 3231937959 at qq.com  Sun Dec 20 02:19:15 2020
From: 3231937959 at qq.com (=?gb18030?B?wfXPsL3c?=)
Date: Sun, 20 Dec 2020 09:19:15 +0800
Subject: [Simnibs-discuss] about display result in deeper area
Message-ID: <tencent_209F2C56BA33A7CF4CBBA8118E1D20F29205@qq.com>

Hello SIMNIBS community,


I wished I could let the EF go deeper in brain when I design new coils for TMS . I check the design with SIMNIBS but do not know how to find computed result except in the gray matter area. Would you help to tell how to show the result in deeper area? Is there a way to display in cross section? Or&nbsp;&nbsp;which is the numerical result file which I could import and display with Matlab?


Thanks,


JS
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From fabio.masina83 at gmail.com  Sat Dec 19 13:29:33 2020
From: fabio.masina83 at gmail.com (Fabio Masina)
Date: Sat, 19 Dec 2020 13:29:33 +0100
Subject: [Simnibs-discuss] anodal vs. cathodal tDCS but same e-field patterns
Message-ID: <CAPJmCpFota1acjCr69Jp5yO5a-EvQw==MaGgFXtaU==+dw5ZKA@mail.gmail.com>

Dear colleagues,

I tried to perform two tDCS simulations (both setting 2mA) using the
default head model (i.e., Ernie). The electrode positions were:

1st simulation_anodal tDCS (target electrode on F7, return on FP2)
2nd simulation_cathodal tDCS (target electrode on F7, return on FP2)

Basically, I only changed the current direction, by changing the polarity
of the target electrode accordingly to the kind of stimulation (2mA for
anodal tDCS and -2mA for cathodal tDCS).
After launching these simulations separately, I realized that the outputs
were exactly the same. Actually, I would have expected to view two
oppositive outputs. I mean, I would have expected two opposite e-field
patterns. Maybe, am I missing something?

Thanks for any suggestion.

Best.

Fabio
-- 

*Fabio Masina, PhD*

IRCCS, Ospedale San Camillo
Via Alberoni 70, 30126
Venice, Italy
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From axelt at drcmr.dk  Tue Dec 22 10:39:48 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 22 Dec 2020 10:39:48 +0100
Subject: [Simnibs-discuss] anodal vs. cathodal tDCS but same e-field
 patterns
In-Reply-To: <CAPJmCpFota1acjCr69Jp5yO5a-EvQw==MaGgFXtaU==+dw5ZKA@mail.gmail.com>
References: <CAPJmCpFota1acjCr69Jp5yO5a-EvQw==MaGgFXtaU==+dw5ZKA@mail.gmail.com>
Message-ID: <53139c4c-c923-2bbf-1d99-c8778737088e@drcmr.dk>

Dear Fabio,

when you switch from anodal to cathodal stimulation with otherwise 
identical settings, you only change the direction of the currents. 
Everything else stays the same. For example, the electric field strength 
will not be affected by that.

To see the changes, you can look at the "E" instead of "normE" (the 
former are the field vectors; the latter is the field strength, i.e. the 
length of the vectors). E will change the direction. Another way to look 
at the changes is to visualize the component of the field that flows in 
or out of the cortex. This component is usually termed "normal 
component" (https://simnibs.github.io/simnibs/build/html/faq.html).

You can get the normal component when you enable "Interpolate to 
cortical surface" in the simulation options 
(https://simnibs.github.io/simnibs/build/html/tutorial/gui.html). It 
then looks similar to Fig 11A in this paper: 
https://www.biorxiv.org/content/10.1101/500314v1

Best regards,

Axel

On 12/19/2020 1:29 PM, Fabio Masina wrote:
> Dear colleagues,
>
> I tried to perform two tDCS simulations (both setting 2mA) using the 
> default head model (i.e., Ernie). The electrode positions were:
>
> 1st simulation_anodal tDCS (target electrode on F7, return on FP2)
> 2nd simulation_cathodal tDCS (target electrode on F7, return on FP2)
>
> Basically, I only changed the current direction, by changing the 
> polarity of the target electrode accordingly to the kind of 
> stimulation (2mA for anodal tDCS and -2mA for cathodal tDCS).
> After launching these simulations separately, I realized that the 
> outputs were exactly the same. Actually, I would have expected to view 
> two oppositive outputs. I mean, I would have expected two opposite 
> e-field patterns. Maybe, am I missing something?
>
> Thanks for any suggestion.
>
> Best.
>
> Fabio
> -- 
> *Fabio Masina,?PhD
> *
>
> IRCCS, Ospedale San Camillo
> Via Alberoni 70, 30126
> Venice, Italy
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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From axelt at drcmr.dk  Tue Dec 22 10:40:54 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 22 Dec 2020 10:40:54 +0100
Subject: [Simnibs-discuss] I wished to apply SIMNIBS when I put
 electrodes inside a skull.
In-Reply-To: <tencent_FB2DD829234DF83F63473AFFFACEB4371A09@qq.com>
References: <tencent_FB2DD829234DF83F63473AFFFACEB4371A09@qq.com>
Message-ID: <c0e8162a-7831-66b0-fae6-0406dc0b7eb6@drcmr.dk>

Dear JS,

unfortunately, SimNIBS does currently not support electrodes inside the 
head. It would be great to add this feature, but we don't have a 
timeline on when to do that.

Best regards,

Axel


On 12/19/2020 4:12 PM, ??? wrote:
> Hi Oula and all SIMNIBS community,
>
> Thank you for taking time to reply my last email.
>
> 1) When I say under the skull, I mean I wished put? electrodes inside 
> skull, or intra-cranial?electrodes.? We can reduce current if 
> electrodes are put into skull. I hope I could compare their? EF on the 
> scalp vs inside skull.
>
> 2) I also wish to apply? SIMNIBS for Deep brain stimulation (DBS) 
> simulation. In this case, electrodes are also inside a skull.
>
> If SIMNIBS does not allow electrodes sitting inside a skull, will you 
> have a plan to update SIMNIBS to meet this new need? and When, if you 
> will have the plan. If you will not do it, will you like to give me 
> some suggestions so that I could follow your sugestion to update?
>
> Your reply are great helps.
>
> JS
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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From axelt at drcmr.dk  Tue Dec 22 10:52:18 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 22 Dec 2020 10:52:18 +0100
Subject: [Simnibs-discuss] about display result in deeper area
In-Reply-To: <tencent_209F2C56BA33A7CF4CBBA8118E1D20F29205@qq.com>
References: <tencent_209F2C56BA33A7CF4CBBA8118E1D20F29205@qq.com>
Message-ID: <e4a58593-2218-03fa-1d52-4bb47d8cec69@drcmr.dk>

Dear JS,

in gmsh: You can look at the results in the gray matter and white matter 
volumes in gmsh. Please see notes on "Visibility" on 
https://simnibs.github.io/simnibs/build/html/tutorial/visualization.html 
and select element numbers 1 and 2 for white and gray matter. Once this 
is shown, you can cut it as you like (see "Clipping" on 
https://simnibs.github.io/simnibs/build/html/tutorial/visualization.html).

gmsh is very flexible, but has some initial learning curve.

Alternatively, you can select "Interpolate to a nifiti volume" when you 
set up a simulation (see 
https://simnibs.github.io/simnibs/build/html/tutorial/gui.html). Then, 
the results will be also saved as nifti-files in the subfolder 
"subject_volumes" of each simulation and you can use any nifti-viewer to 
look at your results.

Best regards,

Axel

/
/



On 12/20/2020 2:19 AM, ??? wrote:
> Hello SIMNIBS community,
>
> I wished I could let the EF go deeper in brain when I design new coils 
> for TMS . I check the design with SIMNIBS but do not know how to find 
> computed result except in the gray matter area. Would you help to tell 
> how to show the result in deeper area? Is there a way to display in 
> cross section? Or which is the numerical result file which I could 
> import and display with Matlab?
>
> Thanks,
>
> JS
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Associate Professor
Danish Research Center for Magnetic Resonance
Copenhagen University Hospital Hvidovre
DK-2650 Hvidovre, Denmark
www.drcmr.dk
&
Department of Health Technology
Technical University of Denmark
DK-2800 Kgs. Lyngby
http://www.healthtech.dtu.dk/

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