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ins-amu / tvb-pipeline

INS TNG pipeline for TVB simulations
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About DWI datasets and some parameter representations #2

Closed nana-zhang closed 2 years ago

nana-zhang commented 2 years ago

Hello, I'm trying to use this library to generate connection matrix and SEEG gain matrix, but I still have some questions. 1. Does DWI data only include DWI file? and do I need.bval and .bvec files? 2. What data is needed to generate the gain matrix?I don't know what data ELEC, ELEC_ENDPOINTS and ELEC_POS_GARDEL represent.

maedoc commented 2 years ago

You can see some of the defaults here.

The DWI data can be a directory of DICOM files, or anything else that the MRtrix3 command mrconvert can handle. I'd recommend doing this conversion to .mif format first.

The ELEC variables specify an image with the contacts and alternatively the endpoints of the sEEG electrodes or the individual positions. This is less well documented since each user may need to customize the code.

nana-zhang commented 2 years ago

Hello, thank you very much for your reply, so it is better to convert DWI data into .mif format, right? As for the electrode data, I already have the positions of each contact of the electrode, so I can directly use it as input data, right?

Can you pay attention to my the other issue? Thank you!

maedoc commented 2 years ago

I would convert to mif yes. You can put the positions of contacts into a txt file which is read with the ELEC_POS_GARDEL option, though it's best to double check the relevant Python code to make sure it's being interpreted correctly.