Surface simulation with HCP data

[Bahar Hazal Yalçınkaya]

Hi,

I am trying to run a Surface simulation for HCP data which I ran through the pipeline (https://github.com/ins-amu/scripts), I use simulate_surface_seeg_eeg_meg.ipynb as a template I calculated vertex_normals for surface data. I successfully upload my corresponding connectome, cortex, and region mapping data but encounter the below error. 

Any ideas?

Thanks in advance,

Kind regards,

Bahar.

[Julie Courtiol]

Hi Bahar,

First, I would suggest you to use in the future the updated version of the scripts pipeline: TVB recon, available here:

https://github.com/the-virtual-brain/tvb-recon

Regarding your question, it is a bit difficult to answer without seeing the code. However, it seems to be a dimensional error with the number of regions. Here 69, instead of 68 I suppose (?).

Hope this helps a bit.

Best, Julie

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Best regards,

Julie Courtiol

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[WOODMAN Michael]

Hi

Did you check your T1 - DWI registration? Did you check the label image step?  Does your tck2connectome step complain that some regions have no tracks?  69 is an unexpected number of regions, which can happen if your label image isn’t registered to the DWI space correctly or isn’t itself correct. 

Cheers

Marmaduke Woodman, TVB Engineer, INS AMU; +33 4 91 32 42 38 +33 7 67 77 84 72

On 9 Sep 2020, at 19:20, Bahar Hazal Yalçınkaya <baharhazal...@gmail.com> wrote:

Hi,

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<Screen Shot 2020-09-09 at 20.10.35.png>

[John Griffiths]

69 also sounds like it wants to be a 68 region parcellation. 

Maybe trying to use matlab indexing on a python array? 

Often you need to subtract 1 from parcellation values intended for matlab for lookup to work correctly in python. 

[Bahar Hazal Yalçınkaya]

Hi,

Thank you for all suggestions. I will try TVB recon for further analysis. 

I actually use the pipeline as it is only set some parameters.

Did you check your T1 - DWI registration? What I understand is registration is related to FSL and the pipeline offer some options as below:

Methods for the FLIRT registration options: ["regular"/"boundary"/"pseudo"]; default: "regular"export REGISTRATION="regular"

Did you check the label image step? I am not sure what should I check it uses "desikan" MR brain image labeling

Does your tck2connectome step complain that some regions have no tracks?

No, it did not.

Actually I have 88 regions. I have one region named after "unknown" may it be related? 

Kind regards,

Bahar. 

John Griffiths <j.davidg...@gmail.com>, 9 Eyl 2020 Çar, 23:27 tarihinde şunu yazdı:

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Ph.D. Bahar Hazal Yalçınkaya

[WOODMAN Michael]

hi

With HCP data you can safely drop the “unknown” region, which may be the source fo the shape mismatch.

Cheers,