Summary

• Page properties (2 modified, 0 added, 0 removed)
• Attachments (0 modified, 2 added, 0 removed)
  • 8677353.png
  • 8d975cf4-13ec-4a6d-9fd9-064bd1fac7b0.jpeg

Details

Page properties

Tags

...	...	@@ -1,0 +1,1 @@
	1	+tool|CHARITE|Simulation|tvb|visualisation|open source|analysis|supercomputer|brain model|neuroinformatics|image processing|the virtual brain

Content

...	...	@@ -5,6 +5,31 @@
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"]] ==
8	8	)))
9	9	)))
10	10
...	...	@@ -12,7 +12,7 @@
12	12	(((
13	13	(% class="col-xs-12 col-sm-8" %)
14	14	(((
15		-= What can I find here? =
	40	+== What can I find here? ==
16	16
17	17	* an IPython notebook that describes how to
18	18	** use the TVB pipeline on one of the associated supercomputers using PyUnicore
...	...	@@ -19,6 +19,16 @@
19	19	** upload model data to the supercomputer
20	20	** set up and run the pipeline
21	21	** 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'"
22	22	)))
23	23
24	24

8677353.png

Author

...	...	@@ -1,0 +1,1 @@
	1	+XWiki.michaels

Size

...	...	@@ -1,0 +1,1 @@
	1	+227.9 KB

Content

8d975cf4-13ec-4a6d-9fd9-064bd1fac7b0.jpeg

Author

...	...	@@ -1,0 +1,1 @@
	1	+XWiki.michaels

Size

...	...	@@ -1,0 +1,1 @@
	1	+107.1 KB

Content