Changes for page TVB PIPELINE
Last modified by ldomide on 2024/05/20 08:56
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... ... @@ -1,1 +1,0 @@ 1 -tool|CHARITE|Simulation|tvb|visualisation|open source|analysis|supercomputer|brain model|neuroinformatics|image processing|the virtual brain - Content
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... ... @@ -5,31 +5,6 @@ 5 5 = From MRI to Functional and Structural Connectivity = 6 6 7 7 Neuroimaging data preprocessing pipeline 8 - 9 -[[image:8677353.png||style="float:left"]] 10 - 11 -(% class="wikigeneratedid" %) 12 -== == 13 - 14 -(% class="wikigeneratedid" %) 15 -== == 16 - 17 -(% class="wikigeneratedid" %) 18 -== == 19 - 20 -(% class="wikigeneratedid" %) 21 -== == 22 - 23 -(% class="wikigeneratedid" %) 24 -== == 25 - 26 -(% class="wikigeneratedid" %) 27 -== == 28 - 29 -(% class="wikigeneratedid" %) 30 -== == 31 - 32 -== [[Pipeline Video Tutorial>>https://drive.google.com/file/d/1VcXf3GX3KoihF4UzJQXzuGL4XWoqj5Jr/view||rel="noopener noreferrer" target="_blank"]] == 33 33 ))) 34 34 ))) 35 35 ... ... @@ -37,7 +37,7 @@ 37 37 ((( 38 38 (% class="col-xs-12 col-sm-8" %) 39 39 ((( 40 -= =What can I find here? ==15 += What can I find here? = 41 41 42 42 * an IPython notebook that describes how to 43 43 ** use the TVB pipeline on one of the associated supercomputers using PyUnicore ... ... @@ -44,16 +44,6 @@ 44 44 ** upload model data to the supercomputer 45 45 ** set up and run the pipeline 46 46 ** download processing results 47 - 48 -== How do I use it? == 49 - 50 -* the pipeline is implemented by three Docker containers (mrtrix3_connectome, fmriprep and tvb_converter) 51 -* the containers are executed on supercomputers and operated via IPython notebooks 52 -* Find the notebook by clicking on "Drive" in the left menu. The notebook is located in the folder "notebooks" 53 -* 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]] 54 -* To use the notebook, download it onto your local filesystem, create a new Collab and upload it there. 55 -* Then, head over to [[https:~~/~~/lab.ebrains.eu/>>url:https://lab.ebrains.eu/||rel="noopener noreferrer" target="_blank"]] to edit and run your notebook. 56 -* 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'" 57 57 ))) 58 58 59 59
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