From giacomo.bertazzoli at unitn.it  Fri Sep  3 11:33:21 2021
From: giacomo.bertazzoli at unitn.it (Giacomo Bertazzoli)
Date: Fri, 3 Sep 2021 11:33:21 +0200
Subject: [Simnibs-discuss] matsimnibs matrix and angles
Message-ID: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>

Dear all,
We would like to know how the output *affine transformation matrix*
(matsimnibs) is obtained when simulating the efield or when doing the coil
optimization. In particular we do not understand if that matrix is the
result of multiple rotations and in the case in which order they occur (we
supposed z-x-y). We need this information because we are trying to assess
the difference (in angle) between two coil positions.
All the very best,

Giacomo

-- 
Giacomo Bertazzoli, PhD Candidate
Cognition Neurostimulation & Connectivity Lab - CIMeC
University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy
Email: giacomo.bertazzoli at unitn.it
https://webapps.unitn.it/du/en/Persona/PER0194098
https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/
<https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/>
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From fang.cao at regionh.dk  Mon Sep  6 09:53:19 2021
From: fang.cao at regionh.dk (Fang Cao)
Date: Mon, 6 Sep 2021 07:53:19 +0000
Subject: [Simnibs-discuss] matsimnibs matrix and angles
In-Reply-To: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>
References: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>
Message-ID: <AS8PR08MB688615018C71CE147C0AD9D9E6D29@AS8PR08MB6886.eurprd08.prod.outlook.com>

Dear Giacomo,

The coordinate system used in Simnibs is defined as the first figure (left) in the attached pdf file. Please let me know if you need more information from us.

Very best,
Fang
________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Giacomo Bertazzoli <giacomo.bertazzoli at unitn.it>
Sent: Friday, 3 September 2021 11.33
To: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk>
Subject: [Simnibs-discuss] matsimnibs matrix and angles

Dear all,
We would like to know how the output affine transformation matrix (matsimnibs) is obtained when simulating the efield or when doing the coil optimization. In particular we do not understand if that matrix is the result of multiple rotations and in the case in which order they occur (we supposed z-x-y). We need this information because we are trying to assess the difference (in angle) between two coil positions.
All the very best,

Giacomo

--
Giacomo Bertazzoli, PhD Candidate
Cognition Neurostimulation & Connectivity Lab - CIMeC
University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy
Email: giacomo.bertazzoli at unitn.it<mailto:giacomo.bertazzoli at unitn.it>
https://webapps.unitn.it/du/en/Persona/PER0194098
https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/ <https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/>

________________________________


Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan laese mere om form?let med anvendelsen samt dine rettigheder p? vores hjemmeside: www.regionh.dk/persondatapolitik
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From kristofferm at drcmr.dk  Mon Sep  6 10:26:09 2021
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Mon, 6 Sep 2021 10:26:09 +0200
Subject: [Simnibs-discuss] matsimnibs matrix and angles
In-Reply-To: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>
References: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>
Message-ID: <CA+zwqSqag2p7Ghkm-nigxS2wFHP80-3ARBJGffLngys2QJ90-w@mail.gmail.com>

Just to elaborate a bit on Fangs answer when using an affine transformation
no particular order of transformations has to be specified. However, if you
require it to be represented as such you can decompose into any order you
like (there is a solution for any order - but it will be different for each
and unfortunately you have to solve a non-linear system). See for example
https://en.wikipedia.org/wiki/Transformation_matrix.
For solving for one particular order you can see for example:
https://github.com/neurodebian/spm12/blob/master/spm_imatrix.m (Matlab code
unfortunately).

Best,
Kristoffer

On Fri, 3 Sept 2021 at 11:43, Giacomo Bertazzoli <
giacomo.bertazzoli at unitn.it> wrote:

> Dear all,
> We would like to know how the output *affine transformation matrix*
> (matsimnibs) is obtained when simulating the efield or when doing the coil
> optimization. In particular we do not understand if that matrix is the
> result of multiple rotations and in the case in which order they occur (we
> supposed z-x-y). We need this information because we are trying to assess
> the difference (in angle) between two coil positions.
> All the very best,
>
> Giacomo
>
> --
> Giacomo Bertazzoli, PhD Candidate
> Cognition Neurostimulation & Connectivity Lab - CIMeC
> University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy
> Email: giacomo.bertazzoli at unitn.it
> https://webapps.unitn.it/du/en/Persona/PER0194098
> https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/
> <https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From annalisa.schuler at hsancamillo.it  Mon Sep  6 10:40:19 2021
From: annalisa.schuler at hsancamillo.it (Annalisa Schuler)
Date: Mon, 6 Sep 2021 10:40:19 +0200 (CEST)
Subject: [Simnibs-discuss] matsimnibs matrix and angles
In-Reply-To: <AS8PR08MB688615018C71CE147C0AD9D9E6D29@AS8PR08MB6886.eurprd08.prod.outlook.com>
References: <CAABHSLgmr4FRAOKF5NiRcVikyXbi6JXpu=H8dGjbVBjEMDik3w@mail.gmail.com>
 <AS8PR08MB688615018C71CE147C0AD9D9E6D29@AS8PR08MB6886.eurprd08.prod.outlook.com>
Message-ID: <1192873968.417569.1630917619711.JavaMail.zimbra@hsancamillo.it>

Hi Giacomo, 

your question is a bit vague. 
What exactly do you try to achieve? 
Are you using Softaxic? 
I am also playing a bit with the software output and how to feed it into matsimnibs at the moment. 
Maybe we could share some experience? 

Best, 

Anna-Lisa 

Annalisa Schuler 
_______________________________________________ 
SAN CAMILLO IRCCS S.R.L. societ? unipersonale 
soggetta a direzione e coordinamento da parte della 
Fondazione Villa Salus 
Via Alberoni, 70 - 30126 Venezia - Lido 
P.IVA e C.F. 04554270274 - Codice SDI: T04ZHR3 

[ https://hsancamillo.it/ | Sito web ] | [ https://www.facebook.com/SanCamilloIRCCS | Facebook ] | [ https://www.linkedin.com/company/san-camillo-irccs | Linkedin ] | [ https://twitter.com/SanCamilloIRCCS | Twitter ] | [ https://www.instagram.com/irccssancamillo/ | Instagram ] 
[ https://hsancamillo.it/ ] 

[ https://hsancamillo.it/5x1000 ] 


Da: "Fang Cao" <fang.cao at regionh.dk> 
A: "Giacomo Bertazzoli" <giacomo.bertazzoli at unitn.it> 
Cc: "simnibs-discuss at drcmr.dk" <simnibs-discuss at drcmr.dk> 
Inviato: Luned?, 6 settembre 2021 9:53:19 
Oggetto: Re: [Simnibs-discuss] matsimnibs matrix and angles 

Dear Giacomo, 

The coordinate system used in Simnibs is defined as the first figure (left) in the attached pdf file. Please let me know if you need more information from us. 

Very best, 
Fang 

From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Giacomo Bertazzoli <giacomo.bertazzoli at unitn.it> 
Sent: Friday, 3 September 2021 11.33 
To: simnibs-discuss at drcmr.dk <simnibs-discuss at drcmr.dk> 
Subject: [Simnibs-discuss] matsimnibs matrix and angles 
Dear all, 
We would like to know how the output affine transformation matrix (matsimnibs) is obtained when simulating the efield or when doing the coil optimization. In particular we do not understand if that matrix is the result of multiple rotations and in the case in which order they occur (we supposed z-x-y). We need this information because we are trying to assess the difference (in angle) between two coil positions. 
All the very best, 

Giacomo 

-- 
Giacomo Bertazzoli, PhD Candidate 
Cognition Neurostimulation & Connectivity Lab - CIMeC 
University of Trento, Corso Bettini 31, 38068 Rovereto (TN) Italy 
Email: [ mailto:giacomo.bertazzoli at unitn.it | giacomo.bertazzoli at unitn.it ] 
[ https://webapps.unitn.it/du/en/Persona/PER0194098 | https://webapps.unitn.it/du/en/Persona/PER0194098 ] 
[ https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/ | https://www.linkedin.com/in/giacomo-bertazzoli-8737b160/? ] 




Region Hovedstaden anvender de personoplysninger, du giver os i forbindelse med din henvendelse. Du kan l?se mere om form?let med anvendelsen samt dine rettigheder p? vores hjemmeside: www.regionh.dk/persondatapolitik 

_______________________________________________ 
Simnibs-discuss mailing list 
Simnibs-discuss at drcmr.dk 
https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss 
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From Helen.Carlson at albertahealthservices.ca  Thu Sep  9 01:11:51 2021
From: Helen.Carlson at albertahealthservices.ca (Helen Carlson)
Date: Wed, 8 Sep 2021 23:11:51 +0000
Subject: [Simnibs-discuss] Skin and bone segmentation layers too thick in
	young subjects
Message-ID: <MW3PR17MB41542C4DCF6F854E31C6E64883D49@MW3PR17MB4154.namprd17.prod.outlook.com>

Hello SimNIBS experts
Thank-you for the wonderful tool. I have run headreco on a cohort of children (aged between 6-19 years of age) with T1 and T2 images in the hopes of modeling tDCS current density. I have found that the skin segmentation layer is protruding outside of the skull all the way around the head. Also, the bone segmentation layer includes the skin. This issue seems to be worse the younger the children are (6-12 years). I suspect this is because of their very thin skulls and skin. I have tried using headreco all --cat and headreco all --no-cat and it makes very little difference, the skin is still too thick to be accurate for modeling. The older children seem to look better (>13 years old). Do you have any other ideas I can try? I can manually edit the skin and bone layers in ITKSnap but was hoping for a more automated (and less subjective) option.
Thank-you in advance for your help
Helen

________________________________
This message and any attached documents are only for the use of the intended recipient(s), are confidential and may contain privileged information. Any unauthorized review, use, retransmission, or other disclosure is strictly prohibited. If you have received this message in error, please notify the sender immediately, and then delete the original message. Thank you.
________________________________
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From s.beumer at tue.nl  Fri Sep 10 11:09:04 2021
From: s.beumer at tue.nl (Beumer, Steven)
Date: Fri, 10 Sep 2021 09:09:04 +0000
Subject: [Simnibs-discuss] Plot fields on arbitrary slices
Message-ID: <AM0PR09MB3858D9404E62A7E7CE1CADE9E7D69@AM0PR09MB3858.eurprd09.prod.outlook.com>

Dear SimNibs community,

For one of our applications, we are interested in plotting the electric field on a user defined slice through the head volume using MATLAB.
From the documentation, we could not directly find an easy way how to do this. However, we could imagine that this has been done before.
Is there someone who can help us with this problem or guide us in the right direction?

Sincerely,

Steven Beumer MSc
[TUe-logo-descriptor-line-scarlet-rgb]
PhD at the electrical engineering faculty



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From martina.bracco at icm-institute.org  Tue Sep 14 16:17:57 2021
From: martina.bracco at icm-institute.org (BRACCO Martina)
Date: Tue, 14 Sep 2021 14:17:57 +0000
Subject: [Simnibs-discuss] Installation issues
Message-ID: <PR0P264MB0826C40097000441943338A4C1DA9@PR0P264MB0826.FRAP264.PROD.OUTLOOK.COM>

Dear all,

I am encountering some difficulties in installing simNIBS 3.2.3 on my Windows 10.
Please find attached the installation log.
May I ask for your assistance with this?

FYI, I have also tried the installation using Conda (Advanced) and I got the following error message:
__________________________________________________
Pip subprocess error:
ERROR: Could not find a version that satisfies the requirement fmm3dpy==0.0.5 (from versions: none)
ERROR: No matching distribution found for fmm3dpy==0.0.5

failed

CondaEnvException: Pip failed
____________________________________________________

Thanks a lot in advance,
Martina

--
Dr. Martina BRACCO, PhD
Marie-Sk?odowska-Curie Fellow at
Normal and abnormal motor control: movement disorders and experimental therapeutics, MOV'IT team
Frontal functions and pathology, FRONTLAB team
Institut du Cerveau - Paris Brain Institute - ICM
H?pital Piti?, 47 Bd de l'H?pital, 75013 Paris, France




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From sikander.khan at s.unikl.edu.my  Thu Sep 16 10:55:14 2021
From: sikander.khan at s.unikl.edu.my (SIKANDER KHAN)
Date: Thu, 16 Sep 2021 08:55:14 +0000
Subject: [Simnibs-discuss] TACS Simulate with desired frequency in SimNIBS
References: <9ff04546-8347-468f-9f07-88ccdd613ce1@Spark>
Message-ID: <7cc4d981-7054-4f81-83b1-625ac5c7fe18@Spark>

Dear Team,

Kindly guide me about TACS Simulation (Frequency > 1 KHz, Voltage setting and Current),

Waiting anxiously for your reply.

Sikander Khan

PhD(IT),
5248-0221-001
sikander.khan at s.unikl.edu.my

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From SHogg at emvision.com.au  Sun Sep 19 03:28:30 2021
From: SHogg at emvision.com.au (Stephen Hogg)
Date: Sun, 19 Sep 2021 01:28:30 +0000
Subject: [Simnibs-discuss] Adding tumour tissue to mesh
Message-ID: <SY4P282MB22845220DD71F61FB0F51B94F7DF9@SY4P282MB2284.AUSP282.PROD.OUTLOOK.COM>

Hi,

Thanks for making SimNIBS, it's a great program. I was wondering if I could ask a few questions about including pathologies in the outputs. Specifically, I have a region of the brain that I want to overwrite with a tissue type not produced by SimNIBS itself (e.g. tumour tissue). In order to include the tumour tissue in the meshes, do I need to add an extra .nii file in the mask_prep directory after updating the existing masks? If so, are there any considerations I should be aware of? How is the new tissue type incorporated in mesh generation? Hope this isn't a bother, would greatly appreciate any light you could shed on this.

Regards,
Stephen
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From utkarshpancholi6387 at gmail.com  Mon Sep 20 09:18:18 2021
From: utkarshpancholi6387 at gmail.com (Utkarsh Pancholi)
Date: Mon, 20 Sep 2021 12:48:18 +0530
Subject: [Simnibs-discuss] Adding tumour tissue to mesh
In-Reply-To: <SY4P282MB22845220DD71F61FB0F51B94F7DF9@SY4P282MB2284.AUSP282.PROD.OUTLOOK.COM>
References: <SY4P282MB22845220DD71F61FB0F51B94F7DF9@SY4P282MB2284.AUSP282.PROD.OUTLOOK.COM>
Message-ID: <CAFvJZmj-Kgh73O05oOA4f-12BnPBjSDOygcNbcnvmMPqDA24yg@mail.gmail.com>

Hi,

Indeed a great question from Stephen. I would also like to ask a
similar question. Is there any way to include pathological abnormalities
like in Alzheimer's disease and MCI (Loss of Neural tissue mass)?  How we
can relate the generated E-field for validation and their effects on
physiological/ neuronal/ functional changes within the target area.
-----------------------------------------------------------------------------------------------------
UTKARSH V. PANCHOLI



On Mon, Sep 20, 2021 at 12:34 PM Stephen Hogg <SHogg at emvision.com.au> wrote:

> Hi,
>
> Thanks for making SimNIBS, it's a great program. I was wondering if I
> could ask a few questions about including pathologies in the outputs.
> Specifically, I have a region of the brain that I want to overwrite with a
> tissue type not produced by SimNIBS itself (e.g. tumour tissue). In order
> to include the tumour tissue in the meshes, do I need to add an extra .nii
> file in the mask_prep directory after updating the existing masks? If so,
> are there any considerations I should be aware of? How is the new tissue
> type incorporated in mesh generation? Hope this isn't a bother, would
> greatly appreciate any light you could shed on this.
>
> Regards,
> Stephen
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From Catriona.Scrivener at mrc-cbu.cam.ac.uk  Mon Sep 20 12:30:35 2021
From: Catriona.Scrivener at mrc-cbu.cam.ac.uk (Catriona Scrivener)
Date: Mon, 20 Sep 2021 10:30:35 +0000
Subject: [Simnibs-discuss] Basic simNIBS questions
Message-ID: <5a0f7245ce9b430e8a2e96c65a1baf2e@mrc-cbu.cam.ac.uk>

Dear simNIBS,


Thank you for creating such a great tool! I am new to simNIBS and have a few basic questions:


1) I have run segmentation using headreco, which I read should preserve the original coordinates of the structural file. Is it sensible to use target co-ordinates derived using SPM as coordinates for a TMS target in simNIBS? I am hoping that a real world xyz coordinate in SPM is the same as an xyz coordinate in simNIBS.


2) The .txt files created by simNIBS' normalisation to MNI space (e.g. MNI2conform_6DOF) look very different to the normalisation parameters created by SPM12 (e.g. s*seg_sn.mat). Is this expected? In particular, values in the fourth column from SPM range up to ~200, but only up to ~10 from simNIBS. Is there a relationship between these files or should I not attempt to equate them?


3) we want to run simulations for a TMS-fMRI experiment. Are there existing coil files for the MagVenture 'MRi-B91 Air Cooled coil', or should I use one of the others provided?


4) for using the dwi2cond function, does a phase direction of '-y' correspond to an AP direction?


5) is it possible to extract the co-ordinates of EEG electrodes projected from the scalp down onto the brain? i.e. can you extract the co-ordinates of the brain region 'closest' to each electrode?


Kind regards,

Catriona



Catriona Scrivener

Research Associate

MRC Cognition and Brain Sciences Unit

University of Cambridge


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From kristofferm at drcmr.dk  Mon Sep 20 12:53:46 2021
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Mon, 20 Sep 2021 12:53:46 +0200
Subject: [Simnibs-discuss] Installation issues
In-Reply-To: <PR0P264MB0826C40097000441943338A4C1DA9@PR0P264MB0826.FRAP264.PROD.OUTLOOK.COM>
References: <PR0P264MB0826C40097000441943338A4C1DA9@PR0P264MB0826.FRAP264.PROD.OUTLOOK.COM>
Message-ID: <CA+zwqSoXFhQ+vNgvZFwRic+gML+hPgPPGG-A6Bu0X9H8GfRESw@mail.gmail.com>

The installation issue might be caused by your organization enforcing a
particular security profile as the powershell script needs the
-executionpolicy bypass flag.
For the manual/advanced installation are you installing in a new
environment using the supplied yml file according to the guideline as given
below, currently newer versions of Python than the one stated in the yml
file (3.7) does not work as fmm3dpy is not available.

conda env create -f environment_win.yml

conda activate simnibs_env


Best,
Kristoffer

On Mon, 20 Sept 2021 at 09:05, BRACCO Martina <
martina.bracco at icm-institute.org> wrote:

> Dear all,
>
>
>
> I am encountering some difficulties in installing simNIBS 3.2.3 on my
> Windows 10.
>
> Please find attached the installation log.
>
> May I ask for your assistance with this?
>
>
>
> FYI, I have also tried the installation using Conda (Advanced) and I got
> the following error message:
>
> __________________________________________________
>
> *Pip subprocess error:*
>
> *ERROR: Could not find a version that satisfies the requirement
> fmm3dpy==0.0.5 (from versions: none)*
>
> *ERROR: No matching distribution found for fmm3dpy==0.0.5*
>
>
>
> *failed*
>
>
>
> *CondaEnvException: Pip failed*
>
> *____________________________________________________*
>
>
>
> Thanks a lot in advance,
>
> Martina
>
>
>
> --
>
> Dr. Martina BRACCO, PhD
>
> *Marie-Sk?odowska-Curie Fellow *at
>
> Normal and abnormal motor control: movement disorders and experimental
> therapeutics, MOV?IT team
>
> Frontal functions and pathology, FRONTLAB team
>
> Institut du Cerveau - Paris Brain Institute ? ICM
>
> H?pital Piti?, 47 Bd de l'H?pital, 75013 Paris, France
>
>
>
>
>
>
>
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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From kristofferm at drcmr.dk  Mon Sep 20 13:12:15 2021
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Mon, 20 Sep 2021 13:12:15 +0200
Subject: [Simnibs-discuss] TACS Simulate with desired frequency in
	SimNIBS
In-Reply-To: <7cc4d981-7054-4f81-83b1-625ac5c7fe18@Spark>
References: <9ff04546-8347-468f-9f07-88ccdd613ce1@Spark>
 <7cc4d981-7054-4f81-83b1-625ac5c7fe18@Spark>
Message-ID: <CA+zwqSo0P0fCQxbWfogxc5T0EE_ibutqjzmeEvJWQT=su+iduQ@mail.gmail.com>

In simNIBS we don't model TACS per se, but for typical low frequencies that
are relevant for stimulation (and even up to several kHz) we are in the
quasi stationary regime where you simply scale the field with the input
waveform. Typically we would not believe that high frequencies above 500 Hz
lead to stimulation effects unless combined with another closeby frequency
to create temporal interference stimulation which is a separate issue
governed by the non-linear effects of the envelope, so I am afraid I cannot
advise on simulation with high frequencies in general.
Best,
Kristoffer

On Mon, 20 Sept 2021 at 09:05, SIKANDER KHAN <sikander.khan at s.unikl.edu.my>
wrote:

> Dear Team,
>
> Kindly guide me about TACS Simulation (Frequency > 1 KHz, Voltage setting
> and Current),
>
> Waiting anxiously for your reply.
>
> *Sikander Khan*
>
> *PhD(IT),*
> *5248-0221-001*
> sikander.khan at s.unikl.edu.my
>
> _______________________________________________
> Simnibs-discuss mailing list
> Simnibs-discuss at drcmr.dk
> https://mailman.drcmr.dk/mailman/listinfo/simnibs-discuss
>
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