[Simnibs-discuss] manual correction

[Axel Thielscher]

Hi Witold,

regarding your question 1: correct

regarding your question 2: You cannot use SimNIBS to automatically 
optimize electrode position for TI. However, I added a matlab function  
and an example on how to calculate and visualize the TI envelop 
amplitude, so that you can manually test and optimize the montages:

https://github.com/simnibs/simnibs/blob/master/simnibs/matlab/get_maxTI.m

https://github.com/simnibs/simnibs/blob/master/simnibs/examples/simulations/TI.m


Best regards,

Axel


On 8/28/2020 10:20 PM, w.tomasz at sensusmed.pl wrote:
> Hi Oula,
>
> Thanks for your answers and suggestions.
> 1)If I understand correctly, the final headform in the B and B + 
> ranges will be sufficient to calculate the optimal stimulation if I 
> first check with Freesurfer for large deviations in bone and skin 
> mapping ?
>
> 2)Is it possible to use software to calculate appropriate electrode 
> placement for transcranial temporal interference stimulation?
> Of course also to visualize the distribution of the electric field.
> For example, for fields with a frequency of 200 and 210 Hz.
> The area of interest is the L-amygdala.
>
> Best regards,
> Witold
> W dniu 2020-08-19 13:36, Oula Puonti napisał(a):
>> Hi Witold,
>>
>> 1) When using CAT the cortical and white matter surfaces are not
>> generated from the volume files (.nii.gz), but rather the surface
>> files stored in the mask_prerp folder. Thus editing the volume files
>>
>> will have no effect on the cortical or white matter surfaces in the
>> final headmodel. You can, however, edit the CSF, skull, and scalp
>> masks and these edits are propagated to the final head model.
>>
>> If you want to edit the GM and WM masks, please disable CAT12
>> (--no-cat flag). After that the edits on the WM and GM masks will also
>> change the final headmodel.
>>
>> 2) We have not studied this systematically, but in my experience CAT12
>> does a good job even if the grade it assigns is B. That being said,
>> you should still inspect the resulting segmentation for large errors
>> using the
>>
>> headreco check call.
>>
>> 3 & 4) I'm not that experienced with manual edits and the little
>> experience I have is limited to freeview. I've heard people
>> succesfully using ITK snap, but if you find it too difficult, I would
>> consider using freeview through the windows subsystem for linux. It's
>> a bit trickier, but the instructions here are quite clear:
>>
>> https://surfer.nmr.mgh.harvard.edu/fswiki/WindowsSupport
>>
>> Best,
>> Oula
>> -------------------------
>>
>> From: Simnibs-discuss <simnibs-discuss-bounces at drcmr.dk 
>> <mailto:simnibs-discuss-bounces at drcmr.dk>> on behalf of
>> w.tomasz at sensusmed.pl <mailto:w.tomasz at sensusmed.pl> 
>> <w.tomasz at sensusmed.pl <mailto:w.tomasz at sensusmed.pl>>
>> Sent: Tuesday, August 18, 2020 5:37:11 PM
>> To: Guilherme B Saturnino
>> Cc: discuss at simnibs.org <mailto:discuss at simnibs.org>
>> Subject: [Simnibs-discuss] manual correction
>>
>> Hello,
>>
>> I had the pleasure of talking to you for a while at the April webinar
>> on brain modeling after stroke.
>> I am currently researching the use of stimulation in a person with
>> tinnitus with personalized stimulation.
>> I have a question about the manual correction of the brain model (the
>> model created from the t1_mprage_sag and t2_space_dark_fluid_sag_p2
>> images) in the automatic model creation in the CAT report gets results
>> on the B and B + levels.
>> I'm a beginner when it comes to modeling (I am more concerned with
>> NIBS in clinical applications), sorry if my questions are trivial :
>>
>> 1. on the SIMNIBS website, it says that it is not possible to do CAT
>> cuttings, whether in such a system we use "m2m_ernie \ mask_prep \
>> MASK_CAT_WM.nii.gz" or "m2m_ernie \ gm.nii.gz" for manual editing.
>> Does a manual correction make sense in such a situation?
>>
>> 2. From your and your team's experience, how big are the differences
>> in electric field distributions between the B / B + and A-level
>> models?
>>
>> 3.I wanted to use ITK-SNAP for the correction proposed on one of your
>> toutorials but I am a beginner I have a hard time figuring out how to
>> check if (how exactly) the surface contours follow the tissue shapes
>> in the T1w image, with more masks than one .
>>
>> 4. Could you suggest a program other than FS to evaluate the created
>> model? Since I'm a Windows 10 and FS user, it's more complicated here.
>>
>> Thank you very much for your help and your time!
>> Best regards,
>> -- 
>>
>>           Witold Tomasz
>>
>>  psycholog, psychoterapeuta, terapeuta tDCS
>>
>>           Ośrodek psychoterapii i neurorehabilitacji
>>
>>           Sensusmed Witold Tomasz
>>
>>           p:
>>           504288040  m: 789335047
>>
>>           a:
>>           Kraków 30-303
>>
>>           ul.Madalińskiego 3/1
>>
>>           w:
>> www.sensusmed.pl <http://www.sensusmed.pl> [1 
>> <http://www.sensusmed.pl>]  e: w.tomasz at sensusmed.pl 
>> <mailto:w.tomasz at sensusmed.pl>
>>
>>
>>
>> Links:
>> ------
>> [1] http://www.sensusmed.pl
>
> -- 
> 	
> Witold Tomasz
> /psycholog, psychoterapeuta, terapeuta tDCS
> /
> Ośrodek psychoterapii i neurorehabilitacji
> *Sensusmed Witold Tomasz*
> p: 	504288040 m: 789335047
> a: 	Kraków 30-303
> 	ul.Madalińskiego 3/1
> w: 	www.sensusmed.pl <http://www.sensusmed.pl> e: 
> w.tomasz at sensusmed.pl <mailto:w.tomasz at sensusmed.pl>
>
>
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-- 
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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