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Civet outputs

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Xuan Mai PHAM edited this page Jan 12, 2024 · 33 revisions

The original set of 39,207 CIVET outputs of the UK Biobank was constructed for participants with session 2 scans.

  • We have added 4,532 CIVET outputs for the participants with session 3 scans.

  • 43,721 CIVET Outputs have been extended with the AAL and DKT atlases. That includes 39,189 outputs for session-2, and 4,532 outputs for session-3.

The data are available to access, visualize and process through CBRAIN but also with the LORIS DQT.

1. Access the CIVET outputs in CBRAIN

CIVET outputs data are directly available to vizualize and process in CBRAIN under the project NeuroHub-UK-Biobank.

From the project page, select the NeuroHub-UK-Biobank, and go to Files. Then, you can filter by type of files and search by name (ses2/ses3/_ses-)

FILE NAME

  • CIVET OUTPUTS session 2 includes files whose names include _ses- and ses2.

Currently, a total of 38,201 + 988 files = 39,189.

  • CIVET OUTPUTS session 3, currently a total of 4,532 files.

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2. Query CIVET outputs with LORIS DQT

CIVET outputs are now available to query with the LORIS DQT and export to NeuroHub.

Note: currently, only ses-2 session (drvd1) is available in the DQT to include derived data.

The CIVET outputs can be found under the following category with their filename as field (collection_filename).

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CIVET outputs DQT process

  • Log in to the LORIS DQT and Create or Load an existing query

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  • Type the category of your query: civet (_civet_outputs__0_1 _will pop out automatically)

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  • Click on collection_filename , select drvd1 and the instances from the file collection you are interested in:

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  • Define filter(s) and add rule(s)

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  • Run Query

Click on Run Query and select your preference as Cross-sectional or Longitudinal

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The results will show up as below:

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  • Export the Query

Once the query is complete, you can download the results in a CSV table or export the results to CBRAIN with the API (refer to Example#3 Export Data to Neurohub). Please choose to export as Civet outputs.

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The CIVET outputs CBRAIN List of files will be created instantaneously:

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NOTE: The CBRAIN file list created will be automatically saved in your default private project. If preferred, you have the option to move it to any other of your project.

  • To view the CIVET outputs file, please click on the Id file link:

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  • You can visualize directly the CIVET outputs on the browser by changing the view and selecting Surface viewer:

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Questions or Issues?

For any questions or issues related to the registration process for accessing the UK Biobank data through the McGill agreement, please contact the NeuroHub team by email at support@neurohub.ca.

For any questions or issues specifically related to accessing the NeuroHub portal or using any of the NeuroHub features and functionalities, please contact the NeuroHub team by email at support@neurohub.ca.

Table of Contents

1. Getting started

  1. Get a NeuroHub account
  2. Obtain UKBiobank access

2. Using NeuroHub

  1. Available Tools and Datasets
  2. Access NeuroHub
  3. Creating a project
  4. LORIS Data Query TooL(DQT)
  5. Jupyter Notebooks in NeuroHub
  6. Messaging in NeuroHub
  7. Accessing the Canadian Open Neuroscience Platform(CONP) datasets
  8. Accessing the HCP(Human Connectome Project) datasets
  9. Accessing the UK Biobank dataset
  10. Accessing the ABCD dataset
  11. Accessing the OpenNeuro dataset

3. Examples

  1. Analyses of structural data
  2. Cellranger Count
  3. scrNAbox
  4. BraTSPipeline

4. Supplementary Information

5. Direct access to the UK Biobank data

  1. Available Data
  2. An example of extracting ICD codes from UK Biobank tabular data
  3. Accessing Imaging Data
  4. Processing Data directly on Beluga

6. NeuroHub and Machine Learning

7. Acknowledging NeuroHub

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