TVB PIPELINE

== [[Direct link to notebook>>https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks||rel="noopener noreferrer" target="_blank"]] ==

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== What can I find here? ==

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* an IPython notebook that describes how to

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** use the TVB processing pipeline on one of the associated supercomputers using PyUnicore

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** upload MRI data to the supercomputer

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** set up and run the pipeline

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** download processing results

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== What does the TVB processing pipeline do? ==

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After uploading MRI data to the supercomputer, the pipeline runs the three containers

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* [[bids/mrtrix3_connectome>>https://hub.docker.com/r/bids/mrtrix3_connectome||rel=" noopener noreferrer" target="_blank"]]

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* [[poldracklab/fmriprep>>https://hub.docker.com/r/poldracklab/fmriprep||rel=" noopener noreferrer" target="_blank"]], and

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* [[thevirtualbrain/tvb_converter>>https://hub.docker.com/r/thevirtualbrain/tvb_converter||rel=" noopener noreferrer" target="_blank"]]

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The TVB Processing Pipeline takes multimodal MRI data sets (anatomical, functional and diffusion-weighted MRI) as input and generates SCs, region-average fMRI time series, FCs, brain surfaces, electrode positions, lead field matrices, and atlas parcellations as output. The pipeline performs preprocessing and distortion-correction on MRI data as well as white matter fiber bundle tractography on diffusion data. Outputs are formatted according to two data standards: a TVB-ready data set that can be directly used to simulate brain network models and the same output in BIDS format.

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== How do I use it? ==

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* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter)

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* the containers are executed on supercomputers and operated via IPython notebooks

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* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks"

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* Direct link to notebook: [[https:~~/~~/drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks>>url:https://drive.ebrains.eu/#my-libs/lib/42ac27a5-981e-4cf6-8ec5-d67b0c24bf09/notebooks]]

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* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there.

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* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook.

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* Depending on whether you created a public or a private notebook it will be accessible in either "drive/Shared with all" or "drive/Shared with groups'"

== Metadata ==

|=Category|tool

|=Tags|(((

* [[Simulaton>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[TVB>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[visualization>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[open-source>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[analysis>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[supercomputers>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[brain-model>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[neuroinformatics>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[image-segmentation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[simulation>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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* [[The-Virtual-Brain>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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|=Partners|(((

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* Charité Universitätsmedizin Berlin [[CHARITE>>url:https://services.humanbrainproject.eu/software-catalog/catalog/?ctx=97d59245-adce-42c4-8b50-d22587071fcd&ctxstate=search%2Ctvb]]

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|=Maintainers|(((

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* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]

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* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]

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* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]

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|=Contributors|(((

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* [[Petra Ritter>>path:mailto:petra.ritter@charite.de]]

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* [[Michael Schirner>>path:mailto:michael.schirner@charite.de]]

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* [[Paul Triebkorn>>path:mailto:jan-paul.triebkorn@charite.de]]

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|=Homepage|[[https:~~/~~/www.brainsimulation.org>>url:https://www.brainsimulation.org/]]

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|=Documentation|[[https:~~/~~/drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view>>url:https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view]]

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|=Support|[[petra.ritter@charite.de>>path:mailto:petra.ritter@charite.de]]

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|=Source Code|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]

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|=Download Page|[[https:~~/~~/hub.docker.com/r/thevirtualbrain/tvb_converter>>url:https://hub.docker.com/r/thevirtualbrain/tvb_converter]]

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|=License|GPLv3

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|=Current Version|1.0

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|=All Versions|(((