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How to Transfer HRRT Scanning Files

In a nutshell, here is what has to be done:

Create a BIC account
Install a SSH client on the remote host
Connect to the BIC gateway
Assemble the list of files acquired during the scanning session
Initiate the transfer

Create a BIC user account

The 1st step to transfer data acquired on the HRRT is to obtain a user account on BIC systems.
A person from the BIC (Director of Facility, researcher, etc.) that vouches for the future user can make the request.
This request must be made by sending an email to <bicadmin@bic.mni.mcgill.ca>.
We will take care to create the user account and inform the parties involved.

Install a SSH client on the remote host

Once the user account is created, he/she must be able to connect, securely, to the BIC servers.

Read

   http://www.bic.mni.mcgill.ca/Services/HowToLogin

for details.

This requires the installation of the encryption software SSH (Secure Shell) on the remote computer that the new user will use to connect to BIC and perform data transfer - unless it is already installed, which is generally the case for Linux and MacOS platforms. For Windows, free and open source clients are available as mentioned in the above URL. We recommend PuTTY. The link quoted above mentions the site to download PuTTY. Installation must be made by the user himself or persons or organizations responsible for IT resources of their institution.

The SSH software allows the creation of a secured transmission channel: information concerning the user and the transmitted or received data are not publicly visible and are encrypted.

Connect to the BIC gateway

Data transfer can then be undertaken once the remote SSH client is installed and the user has logged in to the BIC, initiating a BIC ssh session. The only host at the BIC that allows remote SSH connections is called ‘login.bic.mni.mcgill.ca’. It acts as a sort of gateway. The URL above explains how to connect to it and what happens upon multiple login attempt failures.

Assemble the list of files acquired during the scanning session

The HRRT data can be retrieved from the storage units by issuing the command

    ~$ find_hrrt <expression>

at the command prompt on a login session on the BIC gateway ‘login.bic.mni.mcgill.ca’, where ‘<expression>’ is a shortcut, or a series of characters such as scan session identifier or a participant name, ie, ‘JeanTremblay’. If you know what are regular expressions, now is the time to use them: ‘ ’<expression>’ can contain a regex. Doing this will greatly reduce the amount of output data from the command. For example, all scanning sessions involving ‘DArisk’ done in February 2016:

    ~$ find_hrrt 'DArisk*Feb2016'
    /hrrt/scans10/DAriskABP3508_DArisk_1152_02Feb2016
    /hrrt/scans10/DAriskFal3508_DArisk_1425_02Feb2016
    /hrrt/scans10/DAriskABP3475_DArisk_1107_15Feb2016
    /hrrt/scans10/DAriskFal3475_DArsik_1518_17Feb2016

If one is interested in the last one, DAriskFal3475_DArsik_1518_17Feb2016, just list the files in the directory:

    ls -la /hrrt/scans10/DAriskFal3475_DArsik_1518_17Feb2016

[output not shown as it is too voluminous].

Initiate the transfer

Once the list of files that make up the acquisition session is assembled, the transfer can be initiated by issuing SCP or SFTP commands on the remote SSH client workstation.