From axelt at drcmr.dk  Tue Nov  3 11:45:25 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 3 Nov 2020 11:45:25 +0100
Subject: [Simnibs-discuss] Fw: Area under electrode
In-Reply-To: <904000539.770698.1602138985852@mail.yahoo.com>
References: <247581136.610825.1602096203093.ref@mail.yahoo.com>
 <247581136.610825.1602096203093@mail.yahoo.com>
 <904000539.770698.1602138985852@mail.yahoo.com>
Message-ID: <2813bef2-1383-d276-0bcf-8344a23a4dac@drcmr.dk>

Dear Ghazaleh,

unfortunately, I do not think that SimNIBS offers any functions that 
might help with that.

Best regards,

Axel

On 10/8/2020 8:36 AM, Ghazale Soleimani wrote:
> Dear Dr Thielscher,
> Dear SimNIBS team,
>
> Many thanks for your great software :)
>
> I have a question about the area under the electrode. For example, I 
> have placed an electrode (circular pad or rectangular) in F3 over the 
> scalp in EEG standard system. I want to find the area under the 
> electrode over the gray matter both in MNI space and subject-specific 
> space. Do you have any suggestions?
>
> Stay healthy,
> Ghazaleh

-- 
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 hc888 at bath.ac.uk  Tue Nov 10 23:16:14 2020
From: hc888 at bath.ac.uk (Harry Corker)
Date: Tue, 10 Nov 2020 22:16:14 +0000
Subject: [Simnibs-discuss] OSError: Could not find tissue probability maps.
Message-ID: <LO2P265MB116722888CB53044B5837C1CCAE90@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>

Dear reader,

I am an undergrad researcher at university investigating tDCS and am enjoying learning with your simnibs software. I was hoping you could help me with an issue I am running into when trying to run headreco. I get the following error...
[cid:8f7db7d3-394a-4e43-95cd-6a95cf15b856]
I have MatLab installed and simnibs. Any help would be much appreciated.
Kind regards,

Harry Corker
University of Bath
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From oupu at dtu.dk  Thu Nov 12 08:32:51 2020
From: oupu at dtu.dk (Oula Puonti)
Date: Thu, 12 Nov 2020 07:32:51 +0000
Subject: [Simnibs-discuss] OSError: Could not find tissue probability
	maps.
In-Reply-To: <LO2P265MB116722888CB53044B5837C1CCAE90@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>
References: <LO2P265MB116722888CB53044B5837C1CCAE90@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>
Message-ID: <445a574eeff54ad9a33b3010e1abb4e3@dtu.dk>

Hi Harry,


Can you send us the log file (headreco_log.html)?


Are you using the latest simnibs version (3.2.1)?


Best,

Oula




________________________________
From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk> on behalf of Harry Corker <hc888 at bath.ac.uk>
Sent: Tuesday, November 10, 2020 11:16:14 PM
To: discuss at simnibs.org
Subject: [Simnibs-discuss] OSError: Could not find tissue probability maps.

Dear reader,

I am an undergrad researcher at university investigating tDCS and am enjoying learning with your simnibs software. I was hoping you could help me with an issue I am running into when trying to run headreco. I get the following error...
[cid:8f7db7d3-394a-4e43-95cd-6a95cf15b856]
I have MatLab installed and simnibs. Any help would be much appreciated.
Kind regards,

Harry Corker
University of Bath
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From adrianna.giuffre1 at ucalgary.ca  Wed Nov 18 19:31:38 2020
From: adrianna.giuffre1 at ucalgary.ca (Adrianna Giuffre)
Date: Wed, 18 Nov 2020 18:31:38 +0000
Subject: [Simnibs-discuss] Simnibs error - could not find tissue probability
	maps
Message-ID: <YTBPR01MB362913145A53297F8C8C6AAFADE10@YTBPR01MB3629.CANPRD01.PROD.OUTLOOK.COM>

Hello

My name is Adrianna Giuffre - I am a PhD candidate at the University of Calgary.
I am using SimNIBS for a current modelling project.
I am having the problems running new head models.

1) I am having troubles running the head models for any of my participants - I keep getting an error message saying : (screen shot attached)

Traceback (most recent call last):

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 13, in <module>

    main()

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", line 10, in main

    headmodel(sys.argv)

  File "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", line 265, in headmodel

    raise OSError('Could not find tissue probability maps.\n'

OSError: Could not find tissue probability maps.

Probably something went wrong with the Matlab call or SPM

My participant folder has an "org" folder with the T1.nii and T2.nii in them.
I have Matlab installed on my computer. I am not sure if it is an error with where SIMNIBS downloads on my computer - it seems to only download under a "user" - as you can see from the screenshot - it is the only application in the application folder. In my generic application folder - simnibs doesn't show up visually - though when I open it through terminal it does. I am not sure if this is why it cannot find the site-packages within simnibs. I also tried changing the permission of the application (chmod options) and did not have any success.

I also tried installing simnibs on another user on my computer and on another Mac computer and got the same error. I have used simnibs before and have never had this error.

I have tried to fix this over the last few days and watched the tutorial videos - I can't seem to fix the problem. I updated simnibs to the current version. I also uninstalled it and tried installing it again and am having the same issue. This problem has only occurred using this version. I previously ran 25 head models on the previous version and did not have any issues.

Attached are all the screen shots of my error messages and the code I am using to run the headmodels.
mvp1.sh is the script I am using. I tried "headreco all" and headreco all --cat". The headreco_log.html file is also attached.

I appreciate your time and help!
Thank you in advance!

Kind regards,
Adrianna

--

Adrianna Giuffre | PhD Candidate (Neurosciences) | CSEP-CPT
University of Calgary
Calgary Pediatric Stroke Program
Alberta Children?s Hospital
28 Oki Drive NW, Calgary, AB, Canada
T3B6A8
403-955-2471
adrianna.giuffre1 at ucalgary.ca
Program website: www.perinatalstroke.com<http://www.perinatalstroke.com>


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From axelt at drcmr.dk  Thu Nov 19 18:15:22 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Thu, 19 Nov 2020 18:15:22 +0100
Subject: [Simnibs-discuss] Simnibs error - could not find tissue
 probability maps
In-Reply-To: <YTBPR01MB362913145A53297F8C8C6AAFADE10@YTBPR01MB3629.CANPRD01.PROD.OUTLOOK.COM>
References: <YTBPR01MB362913145A53297F8C8C6AAFADE10@YTBPR01MB3629.CANPRD01.PROD.OUTLOOK.COM>
Message-ID: <0057f360-71ef-5457-89c6-7bf9c66c549f@drcmr.dk>

Hi Adrianna,


thank you for providing the detailed information. Which OS version do 
you use?

We will see whether we can replicate it on our test Mac. In case it runs 
fine here, I would likely suggest a zoom meeting so that we can have a 
look at the issue together.


Best regards,

Axel


On 11/18/2020 7:31 PM, Adrianna Giuffre wrote:
> Hello
>
> My name is Adrianna Giuffre - I am a PhD candidate at the University 
> of Calgary.
> I am using SimNIBS for a current modelling project.
> I am having the problems running new head models.
>
> 1) I am having troubles running the head models for any of my 
> participants - I keep getting an error message saying : (screen shot 
> attached)
>
> Traceback (most recent call last):
>
> File 
> "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", 
> line 13, in <module>
>
> main()
>
> File 
> "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/cli/headreco.py", 
> line 10, in main
>
> headmodel(sys.argv)
>
> File 
> "/Users/adam_kirton_imaging/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/simnibs/msh/headreco.py", 
> line 265, in headmodel
>
> raise OSError('Could not find tissue probability maps.\n'
>
> OSError: Could not find tissue probability maps.
>
> Probably something went wrong with the Matlab call or SPM
>
>
> My participant folder has an "org" folder with the T1.nii and T2.nii 
> in them.
> I have Matlab installed on my computer. I am not sure if it is an 
> error with where SIMNIBS downloads on my computer - it seems to only 
> download under a "user" - as you can see from the screenshot - it is 
> the only application in the application folder. In my generic 
> application folder - simnibs doesn't show up visually - though when I 
> open it through terminal it does. I am not sure if this is why it 
> cannot find the site-packages within simnibs. I also tried changing 
> the permission of the application (chmod options) and did not have any 
> success.
>
> I also tried installing simnibs on another user on my computer and on 
> another Mac computer and got the same error. I have used simnibs 
> before and have never had this error.
>
> I have tried to fix this over the last few days and watched the 
> tutorial videos - I can't seem to fix the problem. I updated simnibs 
> to the current version. I also uninstalled it and tried installing it 
> again and am having the same issue. This problem has only occurred 
> using this version. I previously ran 25 head models on the previous 
> version and did not have any issues.
>
> Attached are all the screen shots of my error messages and the code I 
> am using to run the headmodels.
> mvp1.sh is the script I am using. I tried "headreco all" and headreco 
> all --cat". The headreco_log.html file is also attached.
>
> I appreciate your time and help!
> Thank you in advance!
>
> Kind regards,
> Adrianna
>
> --
>
> Adrianna Giuffre | PhD Candidate (Neurosciences) | CSEP-CPT
>
> University of Calgary
>
> Calgary Pediatric Stroke Program
>
> Alberta Children?s Hospital
>
> 28 Oki Drive NW, Calgary, AB, Canada
>
> T3B6A8
>
> 403-955-2471
>
> adrianna.giuffre1 at ucalgary.ca
>
> Program website: www.perinatalstroke.com <http://www.perinatalstroke.com>
>
>
>
> _______________________________________________
> 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 mccalled at musc.edu  Mon Nov 23 22:18:39 2020
From: mccalled at musc.edu (Mccalley, Daniel)
Date: Mon, 23 Nov 2020 21:18:39 +0000
Subject: [Simnibs-discuss] Relative influence of cortical surface-based
 parameters on resulting efield model
Message-ID: <BN6PR11MB4004E335725A4B099D54BBF9A5FC0@BN6PR11MB4004.namprd11.prod.outlook.com>

Hi all,

I was wondering how/if different features of the cortical surface are modeled in SIMNIBS.

While I'm sure coil-to-cortex distance accounts for a substantial portion of variance between individual electric field size/strength, I would imagine that local features of the cortex such as cortical thickness, orientation/complexity of gyri and/or sulcal depth are incorporated into the modeling. Are these features somehow weighted or accounted for when modeling electric fields?

If so, what is the relative weighting or contribution of these factors in determining the efield model? or alternatively, is it known what portion of individual variance these features explain?

Best,

Dan McCalley
Medical University of South Carolina
College of Graduate Studies, Neuroscience

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From axelt at drcmr.dk  Tue Nov 24 11:23:09 2020
From: axelt at drcmr.dk (Axel Thielscher)
Date: Tue, 24 Nov 2020 11:23:09 +0100
Subject: [Simnibs-discuss] Relative influence of cortical surface-based
 parameters on resulting efield model
In-Reply-To: <BN6PR11MB4004E335725A4B099D54BBF9A5FC0@BN6PR11MB4004.namprd11.prod.outlook.com>
References: <BN6PR11MB4004E335725A4B099D54BBF9A5FC0@BN6PR11MB4004.namprd11.prod.outlook.com>
Message-ID: <caa35efb-7f7b-8bc5-1e8e-efc1d567188d@drcmr.dk>

Hi Dan,


indeed, the local cortical features which you mentioned will influence 
the electric field. This is implicitly accountd for when you calculate 
the field based on individual head models that have anatomically 
accurate representations of the cortex. So, for calculating the field, 
there is no need to explicitly extract these features.


However, it is a different story when you try to understand which 
features explain how much of the electric field variability between 
subjects. Then, you will have to extract them (using some other program) 
to do a correlation analysis between the features and the field in some 
region of interest.


Best regards,

Axel



On 11/23/2020 10:18 PM, Mccalley, Daniel wrote:
> Hi all,
>
> I was wondering how/if different features of the cortical surface are 
> modeled in SIMNIBS.
>
> While I'm sure coil-to-cortex distance accounts for a substantial 
> portion of variance between individual electric field size/strength, I 
> would imagine that local features of the cortex such as cortical 
> thickness, orientation/complexity of gyri and/or sulcal depth are 
> incorporated into the modeling. Are these features somehow weighted or 
> accounted for when modeling electric fields?
>
> If so, what is the relative weighting or contribution of these factors 
> in determining the efield model? or alternatively, is it known what 
> portion of individual variance these features explain?
>
> Best,
>
> Dan McCalley
> Medical University of South Carolina
> College of Graduate Studies, Neuroscience
>
>
> _______________________________________________
> 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 kristofferm at drcmr.dk  Tue Nov 24 19:18:56 2020
From: kristofferm at drcmr.dk (Kristoffer Madsen)
Date: Tue, 24 Nov 2020 19:18:56 +0100
Subject: [Simnibs-discuss] Dirty workaround for simNIBS 3.2.1 issues with
	Mac OS X Big Sur
Message-ID: <CA+zwqSry_XBK7G8QAhF4vdmrnA0sJ8pRyYvy7kHvwCHH+ffJ7g@mail.gmail.com>

Currently simNIBS 3.2.1 fails due to several changes in the Mac OS X
Big Sur, for the moment an extremely ugly fix is provided below:

1) Run the install normally - then wait until it stalls, kill the
python process - choose let files stay.
(for killing python you can check the pid in a terminal using top,
then write kill pid, where pid is the number from top)

Then run silent install in a terminal:
2) /Users/user/Applications/SimNIBS-3.2/simnibs_env/bin/postinstall_simnibs"
-d  /Users/user/Applications/SimNIBS-3.2 --copy-matlab --setup-links
--no-extra-coils --silent --force
(where user is replaced with your user name)

There will then still be an OpenGL error which prevents the gui from
starting because the location of openGL has changed in Big Sur.
3) To fix that you can edit PyOpenGL file
/Users/user/Applications/SimNIBS-3.2/simnibs_env/lib/python3.7/site-packages/OpenGL/platform/ctypesloader.py
changing line:
    fullName = util.find_library( name )
to
    fullName = '/System/Library/Frameworks/OpenGL.framework/OpenGL'

We would very much appreciate reports on any remaining issues, while
we work on a more permanent fix.

From 1155138422 at link.cuhk.edu.hk  Thu Nov 26 02:14:14 2020
From: 1155138422 at link.cuhk.edu.hk (TI, Chun Hang Eden)
Date: Thu, 26 Nov 2020 01:14:14 +0000
Subject: [Simnibs-discuss] About the usage of custom CAT12 segmentation
Message-ID: <HK2PR03MB425889BA4FC797A0778AAC0FB8F90@HK2PR03MB4258.apcprd03.prod.outlook.com>

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 hc888 at bath.ac.uk  Sun Nov 29 17:36:48 2020
From: hc888 at bath.ac.uk (Harry Corker)
Date: Sun, 29 Nov 2020 16:36:48 +0000
Subject: [Simnibs-discuss] tDCS optimisation
Message-ID: <LO2P265MB1167591D3F7634636C8E0D86CAF60@LO2P265MB1167.GBRP265.PROD.OUTLOOK.COM>

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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