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Bryan Caron edited this page Aug 1, 2023 · 4 revisions

Introduction

This manual provides an introduction to CBRAIN, a web-based platform for storing files and running tasks on them. CBRAIN has been developed by support from CANARIE, in professor Alan Evans' lab at the McConnell Brain Imaging Centre and the McGill Centre for Integrative Neuroscience (MCIN), at McGill University. CBRAIN is easy to use and no computer programming expertise is required. All you need is a web browser (recent versions of Firefox, Safari or Chrome, Internet Explorer) and you don’t need to install any specialized software.

Table of contents

  1. Getting started
  2. Create a project
  3. Upload files
  4. Upload files one by one using Web Browser
  5. Upload files all at once using SFTP server
  6. Start a task
  7. Check the progress of a task
  8. Viewing the output of a finished task
  9. Downloading processed output files form finished task
    1. Download files one by one using Web Browser
    2. Download files all at once using SFTP Server
  10. Optional advanced feature of CBRAIN
  11. Help and technical support
  12. Citation

1. Getting started

i. Getting an account

See your service administrator.

ii. Typical data workflow in CBRAIN

  • Upload your files to CBRAIN
  • Run a task (e.g. "Diagnostics") on your files on CBRAIN
  • Examine your processed output files on CBRAIN
  • Download your output files to your computer

iii. Two Methods for Uploading/Downloading Files in CBRAIN

  • If you just have a few files, you can transfer the files one by one using the web browser.
  • If you have many files, you can might find it more convenient to upload them all at once using a SFTP server.

Note: The typical workflow steps in CBRAIN are different depending on which of these two methods you choose, as explained in sections 3.1 and 3.2 (uploading) or sections 7.1 and 7.2 (downloading).

This guide explains how to carry out the steps of typical data workflow in the order listed above using either method for transferring files and using "Diagnostics" as an example of a task which can be carried out in CBRAIN.

2. Create a project

3. Upload files

Data Providers - Network Storage Space: The files in CBRAIN are stored in a "Data Provider", which is network storage space for files on a computer. This could be on your own computer or on another computer you connect to using CBRAIN.

Two Options for Uploading Files: If you only have a few files to upload, you may find it convenient to upload them one by one (Section 3.1), or if you have many files, to upload them all at once (Section 3.2).

i. Upload files one by one using Web Browser

ii. Upload files all at once using SFTP server

Method 1: Filezilla or another GUI SFTP Client

If you are using Mac, Windows or Linux/Unix Operating systems, we recommend that you use Filezilla or another graphical user interface SFTP Client to transfer files.

  • Instructions for Filezilla:
    • Download and install Filezilla on your computer
    • Select "File" menu, then click on "Site Manager"
    • Select "New Site"
    • Under "General Tab" in "Site Manager"
      • Enter hostname: See your service administrator
      • Enter port number: See your service administrator
      • Select Server Type: SFTP - SSH File Transfer protocol
      • Select Logon Type: NORMAL
      • Enter the username and password for your CBRAIN account /interface-guides/user-guides/images/connect1.png
    • Under "Advanced" tab in "Site Manager"
    • Files on your local computer are listed on the left
    • Files on the remote computer are listed on the right
Method 2: Command line

It is very convenient to use a graphical user interface SFTP Client as described above. However, you also have the option of performing these operations at the command line:

  • cd < name of directory where files will go >
  • sftp -o port=XXX [email protected] (See your service administrator)
  • put *.txt
  • Options can be displayed by entering help into the command line

Common part: Move Files from Temporary Storage SFTP Server to Data Provider

  • Move Files from Temporary Storage SFTP Server to Data Provider
  • Move your files from the temporary server to "MainStore":
    • Click on "Register Files" tab
    • Choose project where the files will go (e.g. "Example")
    • Select "Move the files to Data Provider"
    • Choose Data Provider where the files will go (e.g. "MainStore")
    • Click "Register the files" /interface-guides/user-guides/images/register.png
    • Note that if you register a large number of files, this can take some time

4. Start a task

  • Select the project you created

  • Click on "Files" tab

  • If you don’t want to run a task on all of the files, one method to avoid having to click on each file individually is to search files by name (1), or create a custom filter. Note: that the filter will remain in effect until you clear it, so you may think that files are missing if you forget that it is there. If you want to remove the filter, click on "Clear" link next to "Active Filters".

  • Select all the files you want to run a task on (2) /interface-guides/user-guides/images/select_files.png

  • Steps to Start Task:

    • Click on "Launch Task"
    • Click on drop down menu list to select a task
    • Choose task version and server Note: Once you choose a server, you will get a message with approximate time that it might take to start running. You may choose to switch to a different server if the time estimate is too long. /interface-guides/user-guides/images/select_task.png
    • Enter task parameters for "Diagnostics"
    • You can select the Data Provider on which the result will be saved (1) in the "Task Control" section
    • You can choose some parameters for your task in the "Task Parameters" section. You can click on "Help" (2) link in "Task Parameters" section of window, and there are "Help" links like this whenever you launch a task.
    • Click "Start Diagnostics" (3) /interface-guides/user-guides/images/launch_task.png
    • New task appears

5. Check the progress of a task

6. Viewing the output of a finished task

7. Downloading processed output files from finished task

Follow the same procedure you used for uploading files but in reverse (See Section 3 ). You may find it convenient to download files one by one if you just have a few files (Section 7.1), or if you have many files, to download them all at once (Section 7.2).

i. Download files one by one using Web Browser

ii. Download files all at once using SFTP Server

  • Check boxes for all output files to download (1)
  • Or you may find it easy to use the "Filter" feature to select just the output files to download
  • Note: that you have to click on "Clear" next to "Active Filters" if you want to clear the filter. If you forget this you might come back later and think that files are missing.
  • Click on "File Management" (2)
  • Select a SFTP data provider in this case "SFTP-Brainstorm" from drop down menu (3)
  • Click "Copy Files" (4) /interface-guides/user-guides/images/files_to_download.png
Method 1: Filezilla or other GUI interface SFTP client
  • Open Filezilla (or other) application
  • Use same SFTP settings as before (section (#3.2)), but transfer files in the opposite direction Drag/drop files from SFTP-Brainstorm to your computer
Method 2: Command line SFTP

Use commands to change to the right directory and download files:

  • cd < directory_name_to_download_files >
  • sftp -o port=XXX [email protected] (See your service administrator)
  • get -r *

Note: depending on your system, you may get an error message if you try to download files that haven’t been archived using get -r *. If this is the case, go to "File Management", and click on "(Un)Archive" to archive files. This is a toggle switch, meaning that if a file is unarchived it will archive it, and vice versa. Once archived, copy it to the SFTP server. Then do the following:

  • cd < directory_name_to_download_files >
  • sftp -o port=XXX [email protected] (See your service administrator)
  • get /.tar.gz
Common part: Delete your data from the temporary storage SFTP Server

8. Optional advanced feature of CBRAIN

Data Provider Configured on User’s Computer": This manual describes two different options for uploading/downloading files, either using the web browser or SFTP Server. There is in fact a third option for advanced users, which is to use a Data Provider on your own computer, which makes it easier to transfer files. If you wish to use this option, see your service administrator

9. Help and technical support

Methods for Getting Help:

  • There are "Help" buttons at many places on the on-line system.
  • For descriptions of different tools and their parameters, go to "Resources" menu and click on "Tools".
  • There is a "Help" screen for a particular task, whenever you launch a new task.
  • If you have any questions about using CBRAIN or comments on this guide, you can email support: cbrain-support.mni at mcgill.ca.

10. Citation

If you use CBRAIN to process data, please cite the following publication: Sherif T, Rioux P, Rousseau M-E, Kassis N, Beck N, Adalat R, Das S, Glatard T and Evans AC (2014) CBRAIN: a web-based, distributed computing platform for collaborative neuroimaging research. Front. Neuroinform. 8:54. doi: 10.3389/fninf.2014.00054

Note: original author of this user guide is Athena Buckthought

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