Data in TVB Format

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Hana Ali

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Apr 11, 2023, 2:49:09 PM4/11/23
to TVB Users
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

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Apr 11, 2023, 2:56:33 PM4/11/23
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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.


Best,
Lia.

daniele...@gmail.com

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Apr 11, 2023, 4:09:07 PM4/11/23
to TVB Users
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

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Apr 11, 2023, 4:20:30 PM4/11/23
to TVB Users
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

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Apr 12, 2023, 2:07:40 AM4/12/23
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Hi,

A pre-processing pipeline is documented here:

Best,
Lia

Hana Ali

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Apr 14, 2023, 3:28:11 PM4/14/23
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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

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Apr 16, 2023, 10:37:50 AM4/16/23
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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: 

Is this what you are after?

Hana Ali

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Apr 20, 2023, 6:03:59 AM4/20/23
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Hello,

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

Thanks,
Hana
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