Data in TVB Format

[Hana Ali]

Hello,

I'm rather new to TVB and WBM in general, and I'm struggling a bit trying to create the connectivity for TVB. I have raw data as well as the corresponding SC and FC matrices from another source, but I have no idea how to convert the former to TVB format, or if I can use the latter as my connectivity. Any help is appreciated!

Thank you,

Hana

[Lia Domide]

Hi Hana,

Here you can find simple examples of how TVB expects a Structural Connectivity https://github.com/the-virtual-brain/tvb-data/tree/master/tvb_data/connectivity 

It needs to be a zip with few text files inside.

You can read more about tvb data formats here https://docs.thevirtualbrain.org/manuals/UserGuide/Complete_Dataset_Description.html

Best,

Lia.

[daniele...@gmail.com]

Hello,

Trying to build the structural connectome. I have all raw files in DICOM format ( DTI, T1, CT with SEEG reconstruction) and also have the SEEG time-series. I understand there needs to be some preprocessing done from the doc manual you shared. Is there a specific guideline with steps on how to get from raw data to TVB ready data? I understand you need a 3rd party software to do so, is there one you recommend for Mac users?

Thank you!

Best

Daniel

[Hana Ali]

Hello,

Thank you Lia for your response! I mostly wanted to know if there are any pipelines that TVB provides or any 3rd party software that you're aware of that can convert raw data to the TVB format? I'm not sure if this format is achievable in some simple way I don't know.

Thank you!

Hana

[Lia Domide]

Hi,

A pre-processing pipeline is documented here:

https://ebrains.eu/service/the-virtual-brain#process_mri_data_sets_tvb

Best,

Lia

[Hana Ali]

Hello,

Thank you Lia for your response! I mostly wanted to know if there are any pipelines that TVB provides or any 3rd party software that you're aware of that can convert raw data to the TVB format? I'm not sure if this format is achievable in some simple way I don't know.

Thank you!

Hana

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[Randy McIntosh]

Hi Hana - not sure what more you need beyond what Lia's suggested. There is a more recently pipeline that we've update for TVB that you can get here: 

https://github.com/McIntosh-Lab/tvb-ukbb

Is this what you are after?

[Hana Ali]

Hello,

Thank you all for your response! The pipeline shared by Lia was exactly what I needed, thank you so much :)

Thanks,

Hana