From oulap at drcmr.dk  Tue Oct  4 10:58:14 2022
From: oulap at drcmr.dk (Oula)
Date: Tue, 4 Oct 2022 10:58:14 +0200
Subject: [Simnibs-discuss]
 =?utf-8?q?I_can=C2=B4t_install_Simnibs_in_Windo?= =?utf-8?q?ws_11?=
In-Reply-To: <CAMrAEYu0NpsdGRisS_EbYKzMrEgKJ=Y=0-THNxuNz6H=i=Eaxw@mail.gmail.com>
References: <CAMrAEYu0NpsdGRisS_EbYKzMrEgKJ=Y=0-THNxuNz6H=i=Eaxw@mail.gmail.com>
Message-ID: <38cb3059-01ce-1005-da56-06efc09754af@drcmr.dk>

This was a temporary glitch, the site should be up again.

Best,
Oula


On 9/27/22 09:12, IRENE GARCIA DE LA TORRE wrote:
> image.png
> When I try to download the installer, this message appears.
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
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From oulap at drcmr.dk  Fri Oct  7 09:08:22 2022
From: oulap at drcmr.dk (Oula)
Date: Fri, 7 Oct 2022 09:08:22 +0200
Subject: [Simnibs-discuss] Problem with SimNibs on Linux
In-Reply-To: <CAHSQN2B++nS8Fa=4oHhZRQ5Nu1A8shnyLipP-cUFoYLz6cJHuA@mail.gmail.com>
References: <CAHSQN2B++nS8Fa=4oHhZRQ5Nu1A8shnyLipP-cUFoYLz6cJHuA@mail.gmail.com>
Message-ID: <69624f53-b592-d91c-c4b2-4ca84cc29554@drcmr.dk>

Hi Smeet,

Most of these type of problems occur on clusters/servers when libraries 
are missing as is the case here. I wouldn't say it's that common, but 
does happen occasionally.

If you don't have root access it's probably easiest solution if you ask 
your system admins to install the library.

Best,
Oula


On 10/5/22 19:16, Smeet Dhakecha wrote:
> Hi,
>
> I am smeet dhakecha, I am a student researcher at INI, USC. I?ve been 
> trying to install SimNibs on Linux server, and by the end of the 
> installation, I?ve been getting the message attached below. It says 
> that GNU C library 2.14 is not found. I tried finding a fix online, 
> but since I don?t have the sudo root access, I can?t update the GLIBC 
> to?its newer version 2.14. So, is this issue common, and has anyone 
> ever faced this issue that can help me resolve it?
>
> Thanks!
> Smeet
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From m.lueckel at yahoo.de  Fri Oct  7 12:52:35 2022
From: m.lueckel at yahoo.de (=?UTF-8?Q?Maximilian_L=C3=BCckel?=)
Date: Fri, 7 Oct 2022 10:52:35 +0000 (UTC)
Subject: [Simnibs-discuss] White matter surface
References: <1581748401.9629174.1665139955012.ref@mail.yahoo.com>
Message-ID: <1581748401.9629174.1665139955012@mail.yahoo.com>

Hi,?
is there a straightforward way to also get the white matter surface when running CHARM??

Thanks,?
Max
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From dhakecha at usc.edu  Fri Oct  7 18:13:12 2022
From: dhakecha at usc.edu (Smeet Dhakecha)
Date: Fri, 7 Oct 2022 09:13:12 -0700
Subject: [Simnibs-discuss] Problem with SimNibs on Linux
In-Reply-To: <69624f53-b592-d91c-c4b2-4ca84cc29554@drcmr.dk>
References: <CAHSQN2B++nS8Fa=4oHhZRQ5Nu1A8shnyLipP-cUFoYLz6cJHuA@mail.gmail.com>
 <69624f53-b592-d91c-c4b2-4ca84cc29554@drcmr.dk>
Message-ID: <CAHSQN2DVxKTPzQKsCsuS4+y_znavD7rX48ZX4zzgkM5ONzfzTA@mail.gmail.com>

Hi Oula,

I really appreciate you reaching out. I?ll try asking the Admins for help
to see if they can change the version or anything.

Thanks!
Smeet dhakecha

On Fri, Oct 7, 2022 at 12:08 AM Oula <oulap at drcmr.dk> wrote:

> Hi Smeet,
>
> Most of these type of problems occur on clusters/servers when libraries
> are missing as is the case here. I wouldn't say it's that common, but does
> happen occasionally.
>
> If you don't have root access it's probably easiest solution if you ask
> your system admins to install the library.
>
> Best,
> Oula
>
>
> On 10/5/22 19:16, Smeet Dhakecha wrote:
>
> Hi,
>
> I am smeet dhakecha, I am a student researcher at INI, USC. I?ve been
> trying to install SimNibs on Linux server, and by the end of the
> installation, I?ve been getting the message attached below. It says that
> GNU C library 2.14 is not found. I tried finding a fix online, but since I
> don?t have the sudo root access, I can?t update the GLIBC to its newer
> version 2.14. So, is this issue common, and has anyone ever faced this
> issue that can help me resolve it?
>
> Thanks!
> Smeet
>
>
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From Morgan.Thienpont at UGent.be  Sat Oct  8 15:18:32 2022
From: Morgan.Thienpont at UGent.be (Morgan Thienpont)
Date: Sat, 8 Oct 2022 13:18:32 +0000
Subject: [Simnibs-discuss] T1+FLAIR+segmentation
Message-ID: <AM9PR09MB465845AFF1C63BD5C8C26BDDF35E9@AM9PR09MB4658.eurprd09.prod.outlook.com>

Dear

I have a question concering the use of headreco.
Is it possible to use headreco when a T1 and FLAIR image are given, but also that specific segmentations (by .MS pathology specific toolboxes) that are already made, can be used?

I can see in the manual that masks can be added, but not how segmentations can be added?

Thanks in advance and kind regards
Morgan Thienpont
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From axelt at drcmr.dk  Tue Oct 11 13:06:43 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 11 Oct 2022 13:06:43 +0200
Subject: [Simnibs-discuss] White matter surface
In-Reply-To: <1581748401.9629174.1665139955012@mail.yahoo.com>
References: <1581748401.9629174.1665139955012.ref@mail.yahoo.com>
 <1581748401.9629174.1665139955012@mail.yahoo.com>
Message-ID: <6a09028f-3e1f-14e8-ac03-0b29539bde16@drcmr.dk>

Hi Max,

you can load the final mesh and extract the WM surface from it, e.g. in 
python:

from simnibs import mesh_io
m = mesh_io.read_msh('ernie.msh')
m = m.crop_mesh(tags=1001)
mesh_io.write_msh(m,'ernie_wm.msh')

Best,

Axel


On 07-10-2022 12:52, Maximilian L?ckel wrote:
> Hi,
>
> is there a straightforward way to also get the white matter surface 
> when running CHARM?
>
>
> Thanks,
>
> Max
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
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 Oct 11 13:11:04 2022
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 11 Oct 2022 13:11:04 +0200
Subject: [Simnibs-discuss] Use head mesh obtained from FreeSurfer
In-Reply-To: <DBAP195MB10046DC1DBC0E4AEA501B975FB559@DBAP195MB1004.EURP195.PROD.OUTLOOK.COM>
References: <DBAP195MB10046DC1DBC0E4AEA501B975FB559@DBAP195MB1004.EURP195.PROD.OUTLOOK.COM>
Message-ID: <846e7bea-d7ac-25ec-b92d-31977b5482fa@drcmr.dk>

Hi Silvana,

I haven't worked with TVB on my own. From an earlier request, it seems 
that TVB also has tissue masks as nifti-volumes. Then you don't need 
surfaces to create a head model.

You just have to create one nifti file where the compartment labels 
follow the simnibs conventions: 1 WM, 2 GM, 3 CSF, 4 SKULL, 5 SKIN. If 
you would like to distinguish between more comparments, let me know.

The run the /meshmesh /command of simnibs4 
(https://github.com/simnibs/simnibs/releases/tag/v4.0-beta1) to get a 
volume mesh for field simulations.

Hope this helps.

Best regards,

Axel

On 27-09-2022 16:27, Huertas Penen, Silvana (UT-EEMCS) wrote:
>
> Hi everyone,
>
> I?m working with The virtual brain (TVB) and SimNibs, and I need to be 
> able to use the head mesh from TVB in SimNIBS.
>
> The head mesh from TVB is calculated using FreeSufer. Do you have any 
> clue if I can use the mesh obtained from Freesurfer in SimNIBS?
>
> The FreeSurfer gives me the mesh in zip files, having face and vertex 
> information.
>
> Kind regards,
>
> Silvana
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss

-- 
Dr. Axel Thielscher
Professor of Neurophysics and Neuroimaging
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 oulap at drcmr.dk  Tue Oct 11 15:08:36 2022
From: oulap at drcmr.dk (Oula)
Date: Tue, 11 Oct 2022 15:08:36 +0200
Subject: [Simnibs-discuss] T1+FLAIR+segmentation
In-Reply-To: <AM9PR09MB465845AFF1C63BD5C8C26BDDF35E9@AM9PR09MB4658.eurprd09.prod.outlook.com>
References: <AM9PR09MB465845AFF1C63BD5C8C26BDDF35E9@AM9PR09MB4658.eurprd09.prod.outlook.com>
Message-ID: <115f1250-c2fa-efd5-8b5f-8d6707253e03@drcmr.dk>

Hi Morgan,


I suggest you try the new version of Simnibs (v4-beta), which is 
available here:


https://github.com/simnibs/simnibs/releases


Adding extra tissues and modifying the FEM mesh is much easier in the 
new version. Please see the documentation after having installed the new 
version.


Best,
Oula



On 10/8/22 15:18, Morgan Thienpont wrote:
> Dear
>
> I have a question concering the use of headreco.
> Is it possible to use headreco when a T1 and FLAIR image are given, 
> but also that specific segmentations (by .MS pathology specific 
> toolboxes) that are already made, can be used?
>
> I can see in the manual that masks can be added, but not how 
> segmentations can be added?
>
> Thanks in advance and kind regards
> Morgan Thienpont
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
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From oulap at drcmr.dk  Tue Oct 11 15:13:33 2022
From: oulap at drcmr.dk (Oula)
Date: Tue, 11 Oct 2022 15:13:33 +0200
Subject: [Simnibs-discuss] How to simulate dual-site tACS with random
 phase shift?
In-Reply-To: <CAG1p7rhiZh7d_yqZuFR7WnHf_bd5UHZO0uOzNcW15BccsCH6Gg@mail.gmail.com>
References: <CAG1p7rhiZh7d_yqZuFR7WnHf_bd5UHZO0uOzNcW15BccsCH6Gg@mail.gmail.com>
Message-ID: <82f8154d-db7c-e932-b2ac-beabb643e77c@drcmr.dk>

Hi Jinwen,

To get started please see this paper:

https://www.sciencedirect.com/science/article/abs/pii/S1053811917307723

which goes through some specific examples of how to simulate tACS with 
SimNIBS.

Best,

Oula


On 9/10/22 05:37, Jinwen Wei wrote:
> Dear simNIBS experts and users,
>
> How to simulate the electric field during dual-site tACS with random 
> phase shift using simNIBS? I have seen dual-site tACS with phase shift 
> of 45?/135? could generate "traveling wave" electric field dynamics in 
> this study: Alekseichuk, I., Falchier, A. Y., Linn, G., Xu, T., 
> Milham, M. P., Schroeder, C. E., & Opitz, A. (2019). Electric field 
> dynamics in the brain during multi-electrode transcranial electric 
> stimulation. /Nature communications/, /10/(1), 1-10.
>
> However, I could only find a few hints about simulating electric field 
> generated by dual-site tACS by simNIBS, not to mention with random 
> phase shift. Could anyone tell me how to start?
>
> Best regards,
> Jinwen
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
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From oulap at drcmr.dk  Tue Oct 11 15:19:35 2022
From: oulap at drcmr.dk (Oula)
Date: Tue, 11 Oct 2022 15:19:35 +0200
Subject: [Simnibs-discuss] ROI drawing
In-Reply-To: <OS3P286MB1589EC496F1019E22E1E2AA2CA7A9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
References: <OS3P286MB1589EC496F1019E22E1E2AA2CA7A9@OS3P286MB1589.JPNP286.PROD.OUTLOOK.COM>
Message-ID: <d1770be9-8ab5-f635-b1db-739acc7f80a2@drcmr.dk>

Hi Bella,

It's a bit tricky to draw on the surfaces directly.

What you could do is to run the simulations with map_to_surf set to 
true, so that the e-field is interpolated onto the middle gray matter 
surface. After that, draw the ROI on the MRI volume, i.e., manually 
create a ROI mask using for example freeview. Once you have that, you 
can use freesurfer's mri_vol2surf to map the volume ROI onto the middle 
gray matter surface, and visualize/analyze the e-field within the ROI.


Best,
Oula


On 9/2/22 14:32, ZHANG, bellabingbing [Student] wrote:
> Dear Dr. Thielscher,
>
> I am a Ph.D student from the Hong Kong Polytechnic University. We 
> recently submitted an article to a juornal. However, the reviewer 
> suggests we draw the ROI on the figure. Therefore, I would like to 
> visualize the ROI on the brain surface after the E_field simulation as 
> follows. Do you have any suggestions how could I do this?
>
>
> Best Regards,
> Bella ZHANG
>
>
> /Disclaimer:/
>
> /This message (including any attachments) contains confidential 
> information intended for a specific individual and purpose. If you are 
> not the intended recipient, you should delete this message and notify 
> the sender and The Hong Kong Polytechnic University (the University) 
> immediately. Any disclosure, copying, or distribution of this message, 
> or the taking of any action based on it, is strictly prohibited and 
> may be unlawful./
>
> /The University specifically denies any responsibility for the 
> accuracy or quality of information obtained through University E-mail 
> Facilities. Any views and opinions expressed are only those of the 
> author(s) and do not necessarily represent those of the University and 
> the University accepts no liability whatsoever for any losses or 
> damages incurred or caused to any party as a result of the use of such 
> information./
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
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From zhen.li.dada at gmail.com  Mon Oct 17 11:21:45 2022
From: zhen.li.dada at gmail.com (Zhen Li)
Date: Mon, 17 Oct 2022 11:21:45 +0200
Subject: [Simnibs-discuss] Could not find tissue probability maps
Message-ID: <CAL6PzgqhVSTmTfkZiTqZYTrP4fdi3QCxaFmGKawHSTzWAbkVSw@mail.gmail.com>

Dear researchers,

I am using simnibs on ubuntu and have a problem about *"Could not find
tissue probability maps"* when constructing the dead model.
I have uploaded the log file, please find attachment if needed.

I have read the same question about it and I can find T1fs_conform.nii in
the folder,
\danie\m2m_danie\segment\spm.
However I have no idea how to solve this problem.
Could you please provide me with any advice? Thank you for your help in
advance!!

Best wishes,
Zhen
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From s.huertaspenen at utwente.nl  Tue Oct 18 07:45:42 2022
From: s.huertaspenen at utwente.nl (Huertas Penen, Silvana (UT-EEMCS))
Date: Tue, 18 Oct 2022 05:45:42 +0000
Subject: [Simnibs-discuss] Downsample surface
Message-ID: <DBAP195MB100447DFBB167DC45A70DA26FB289@DBAP195MB1004.EURP195.PROD.OUTLOOK.COM>

Hi,

I need to have a headmesh in Simnibs with 16k vertices in the surface. This to be able to use the output of simnibs in TVB. What I did was to import the headmesh I did in Simnibs to Brainstorm and then downsample to 16k. Now I have the surface downsampled but I do not know how to input/merge this with the headmesh I made in SimNibs. Do you know how to do this?

Or if there is a method in simnibs to downsample the surface in the headmesh?

Get Outlook for Android<https://aka.ms/AAb9ysg>
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From zhen.li.dada at gmail.com  Tue Oct 18 13:10:11 2022
From: zhen.li.dada at gmail.com (Zhen Li)
Date: Tue, 18 Oct 2022 13:10:11 +0200
Subject: [Simnibs-discuss] Could not find tissue probability maps
Message-ID: <CAL6PzgoRg0OXDDV0mDTX3EDrfZOy98VmB0Shp1hog2fX0v4g0w@mail.gmail.com>

Dear researchers,

I am using simnibs on ubuntu and have a problem about *"Could not find
tissue probability maps"* when constructing the dead model.
I have uploaded the log file, please find attachment if needed.

I have read the same question about it and I can find T1fs_conform.nii in
the folder,
\danie\m2m_danie\segment\spm.
However I have no idea how to solve this problem.
Could you please provide me with any advice? Thank you for your help in
advance!!

Best wishes,
Zhen
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From margaret.mcallister at duke.edu  Wed Oct 19 15:17:03 2022
From: margaret.mcallister at duke.edu (Margaret McAllister)
Date: Wed, 19 Oct 2022 13:17:03 +0000
Subject: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.6,
	Running FSL 6.0.3
In-Reply-To: <BN7PR05MB40501CE6914B6FC7F7DDBFAF9C2B9@BN7PR05MB4050.namprd05.prod.outlook.com>
References: <BN7PR05MB40501CE6914B6FC7F7DDBFAF9C2B9@BN7PR05MB4050.namprd05.prod.outlook.com>
Message-ID: <BN7PR05MB40507824F73BC606376F79039C2B9@BN7PR05MB4050.namprd05.prod.outlook.com>

Ah, I see my mistake. I thought that FSL was the acronym for FreeSurfer. I?ll try running with Free Surfer version<7. Please disregard.

Mags

From: Margaret McAllister <margaret.mcallister at duke.edu>
Date: Wednesday, October 19, 2022 at 9:06 AM
To: discuss at simnibs.org <discuss at simnibs.org>
Subject: Meshfix error in SimNIBS-3.2.6, Running FSL 6.0.3
Hello,


I?m using SimNIBS-3.2.6 to generate head segmentation for a subject. I don?t have a T2 image for this participant. I am using mri2mesh because the scan does not include neck and shoulders. This is the error I encountered.



mris_convert ./opticrad_FS.fsmesh ./opticrad_FS.stl



/usr/local/packages/simnibs/3.2.6/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix subcortical_FS.stl -a 2.0 --remove-handles -q -o subcortical.off



ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed.error code 255

exiting mri2mesh



In the previous discussion (linked below) this error was resolved by using a version of FSL >7. I am running fsl version 6.0.3 so that is not the issue for me.



https://mailman.drcmr.dk/pipermail/simnibs-discuss/2021-April/000205.html



Is there a solution to this issue?



Thanks!

Mags M.

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From margaret.mcallister at duke.edu  Wed Oct 19 15:06:08 2022
From: margaret.mcallister at duke.edu (Margaret McAllister)
Date: Wed, 19 Oct 2022 13:06:08 +0000
Subject: [Simnibs-discuss] Meshfix error in SimNIBS-3.2.6, Running FSL 6.0.3
Message-ID: <BN7PR05MB40501CE6914B6FC7F7DDBFAF9C2B9@BN7PR05MB4050.namprd05.prod.outlook.com>

Hello,


I?m using SimNIBS-3.2.6 to generate head segmentation for a subject. I don?t have a T2 image for this participant. I am using mri2mesh because the scan does not include neck and shoulders. This is the error I encountered.



mris_convert ./opticrad_FS.fsmesh ./opticrad_FS.stl



/usr/local/packages/simnibs/3.2.6/simnibs_env/lib/python3.7/site-packages/simnibs/bin/linux/meshfix subcortical_FS.stl -a 2.0 --remove-handles -q -o subcortical.off



ERROR- fseek /home/guilherme/simnibs_misc/meshfix/contrib/JMeshLib/src/MESH_STRUCTURE/io.cpp:1335 failed.error code 255

exiting mri2mesh



In the previous discussion (linked below) this error was resolved by using a version of FSL >7. I am running fsl version 6.0.3 so that is not the issue for me.



https://mailman.drcmr.dk/pipermail/simnibs-discuss/2021-April/000205.html



Is there a solution to this issue?



Thanks!

Mags M.

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From jupston at unm.edu  Wed Oct 19 21:07:24 2022
From: jupston at unm.edu (Joel Upston)
Date: Wed, 19 Oct 2022 19:07:24 +0000
Subject: [Simnibs-discuss] Differences in Efield depending on Processing
Message-ID: <CY1PR07MB271401D126AA612F026D1102BF2B9@CY1PR07MB2714.namprd07.prod.outlook.com>

Hi there,

I have noticed a systematic difference between the two different lines of simulating the same currents, electrodes and underlying dataset. One is through processing through the leadfield and using only the electrodes and currents as given and the other is through only modeling those electrodes and currents without the leadfield. Now the 2nd pathway (no leadfield) is giving higher E_mag than the leadfield version (~7-12%), the spatial maps look similar but just the intensity differences. I think it has to do with the scaling that is done after the solve by scaling the estimated current calibration error, which if I understand correctly isn't done in the leadfield processing.  If this is the case I am trying to establish which would be more accurate to use in your view if I need a specific target value of (0.3 V/m for example). I have attached an image of a case where this is shown with the leadfield processed is on the left and the non-leadfield is on the right. I have tried this on about 5 different datasets and the pattern is consistent.

Thanks,

Joel
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