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22	22	* Open KG in browser: [[https:~~/~~/kg.ebrains.eu/search/>>url:https://kg.ebrains.eu/search/]]
23	23	* Browse through KG and look for a data set that contains the above-mentioned MRI modalities. To find a suitable data set you may use the “Filter” sidebar on the left and e.g. select “Homo sapiens” or “magnetic resonance imaging”. In the following we are going to use the data set “Individual Brain Charting: ARCHI Social”. [[https:~~/~~/kg.ebrains.eu/search/instances/Dataset/f8c40aadc4939ad493bf7c839b82cb40>>https://kg.ebrains.eu/search/instances/Dataset/f8c40aadc4939ad493bf7c839b82cb40]]
24	24	* The data-set can be downloaded from [[https:~~/~~/openneuro.org/datasets/ds000244/versions/1.0.0>>url:https://openneuro.org/datasets/ds000244/versions/1.0.0]]
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25	25	* Download the imaging data. The full dataset would be quite large: 54.06 GB. It contains several subjects, modalities, tasks and runs, most of which we don’t need to demo the workflow. We will therefore only download the minimal set of files that we need to form a valid BIDS data set and to perform the following steps. Using the Dataset File Tree on the right, download the files indicated in the following folder tree. The interface unfortunately only allows to download individual files, so you have to click each one of them and also you have to create the necessary folder structure (incl. the folders sub-01, anat, dwi, func) yourself. Note that the full data set contains multiple sessions identified by the keyword “ses-XX”, where “XX” indicates the session number. Here we use only data from ses-00 and therefore omit the folder and instead directly copy the folders “dwi”, “func”, and “anat” one level beneath “sub-01”. When you are done, your folder tree should look like this:
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26	26	* We now have an MRI dataset in BIDS format. The next step is to compress the folder (e.g. as a .zip or .tar.gz file) so that we can upload it as a single file to the EBAINS Collaboratory and later to the supercomputer. In the next steps, we are going to use diffusion MRI tractography to reconstruct white matter fiber pathways and to estimate coupling weights between brain regions.
27	27	* Open the TVB Pipeline EBRAINS Collab: [[https:~~/~~/wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline/>>url:https://wiki.ebrains.eu/bin/view/Collabs/tvb-pipeline/]]
28	28	* The pipeline is implemented in the form of a Jupyter notebook that shows how to upload data from local filesystem to EBRAINS drive; how to copy the data to the supercomputer; how to run the three docker containers that perform the processing; how to download results to local filesystem.
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29	29	* In order to use EBRAINS Collab software, it is necessary to download the notebook, create a new Collab, and upload the notebook there. The process is described on the main Collab page and in the notebook.
30	30	* For brain simulation the most important result of tractography is the structural connectome (SC), which consists of the coupling strengths matrix and the distances matrix. The former quantifies the strength of interaction between each pair of brain regions and the latter contains the average length of the respective fiber bundle. The exported SC can be directly imported to TVB: as one of the last steps of the pipeline, the SC was stored along with other data that can be read by TVB in the file "TVB_output.zip". Within that ZIP archive is the file “sub-<participant_label>_Connectome.zip”, which can be used to set up a brain network model in the other TVB workflows.
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32	32	== The Virtual Brain: simulate brain activity ==
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34	34	The Virtual Brain is the main TVB software package. It is a neuroinformatics platform that provides an ecosystem of tools for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivity. TVB can be operated via GUI and programmatic Python interface. On the HBP Collaboratory Platform TVB Simulator usage is introduced through IPython Notebooks. Additionally, the TVB GUI can be directly accessed as a Web App ([[https:~~/~~/thevirtualbrain.apps.hbp.eu/user/profile>>url:https://thevirtualbrain.apps.hbp.eu/user/profile]]). Via the Web App users can configure simulations that are – depending on their complexity – either simulated directly on the web server or on a supercomputer, thereby making resource-consuming TVB functionality accessible to researchers that do not have access to supercomputers. Compiled standalone versions of the main software package can be downloaded from thevirtualbrain.org. In the following we take you through the main steps of brain network model simulation.

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