[Simnibs-discuss] normE values in MNI space

[Jane Tan]

Hi Guilherme,

Ah I see. I have been using v.3.0.6. I will update accordingly.

with thanks,
Jane
________________________________
From: Guilherme B Saturnino <guilhermebs at drcmr.dk>
Sent: Thursday, 19 March 2020 6:32 PM
To: Jane Tan <Jane.Tan at murdoch.edu.au>; discuss at simnibs.org <discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] normE values in MNI space


Which SimNIBS version are you using? In 3.1 we switched to using linear interpolation, so these artifacts should not happen anymore.


Best Regards,

Guilherme



On 19/03/2020 10.31, Jane Tan wrote:
Hi Guilherme,

Thanks for the reply. There are a good number of negative values (~22.5%).
Do you have any suggestions on what I can do to attenuate the artifacts? My main aim is to get the mean e-field for specific ROIs.
For instance, would you recommend the use of normJ instead? I notice that there are fewer negative values for normJ, and notably none in the ROIs I am interested in.

best regards,
Jane
________________________________
From: Guilherme B Saturnino <guilhermebs at drcmr.dk><mailto:guilhermebs at drcmr.dk>
Sent: Thursday, 19 March 2020 4:08 PM
To: Jane Tan <Jane.Tan at murdoch.edu.au><mailto:Jane.Tan at murdoch.edu.au>; discuss at simnibs.org<mailto:discuss at simnibs.org> <discuss at simnibs.org><mailto:discuss at simnibs.org>
Subject: Re: [Simnibs-discuss] normE values in MNI space


Dear Jane,



How many negative values are there? This is likely an artifact due to spline interpolation of the electric field from the original space to MNI space.


Best Regards,

Guilherme


On 19/03/2020 06.06, Jane Tan wrote:
Hi SimNIBS Team,

I found some negative values in my nifti volume for normE in MNI space, and I thought something must have gone awry during the segmentation process for my head mesh (created using headreco (with cat) on a MNI152 T1-weighted image).  However, the head mesh looks okay when I checked it with gmsh. The headreco_log doesn't seem to indicate any issues either - at least not to my untrained eye. I do not have access to freeview, and couldn't do a proper check via headreco.

I'm also wondering if it might be due to normE not being very accurate as a result of registration to the MNI template?

Your suggestions would be greatly appreciated. I am happy to provide my head mesh and segmentation results if that would be of any help.

best regards,
Jane







Best regards,


Jane





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