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fcon 1000:INDI

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Getting INDI to work for you

In contrast to the FCON Classic data, the INDI data will be distributed together with XNAT. This will allow for the easy creation of a database on your local machine that will contain all of the data released through INDI.

We are currently releasing the INDI-XNAT database as a 'virtual machine'. This means that it will run inside a virtual Ubuntu linux application within your existing operating system. It is compatible with Windows, Mac OS, or Linux systems. In order to run the virtual machine, you will need a program called Virtual Box.

BE SURE TO READ THE SECTION BELOW ON WORKING WITH YOUR INDI VIRTUAL MACHINE. Setting up the shared folders as explained there is imperative for proper functioning of the virtual machine.

Request Access to the INDI project

Given the increased amount of information provided in the INDI datasets, we are requiring that individuals register with the 1000 Functional Connectomes Project website on NITRC to gain access to the INDI datasets. Upon successful registration, users will have full access to the datasets, and the right to unrestricted usage of the datasets for non-commercial purposes, just as before.

Registration is a simple process, as follows:

  1. If you have not already established an NITRC user account, you will be required to do so. It is easy to do and free of charge. Join NITRC
  2. Once registered as a NITRC user, request access to the INDI project. Request Access to INDI
  3. In the free text box that appears, enter your name, institution, research level (e.g., grad student, post-doc, research scientist, faculty, etc), email address (we will not use this for any advertisement purposes) and area of expertise.
  4. Click submit – that’s it! Upon receipt of the requested info, you will be granted access by a member of our team. Note that this might take a day!

INDI-XNAT versus INDI-Lite

We are distributing two versions of INDI.

  1. INDI-XNAT uses full XNAT database
  2. INDI-Lite does not include the XNAT database. (It DOES include all data)

For each release we will provide both INDI-XNAT and INDI-Lite.

INDI-XNAT

This release includes all data, both imaging and phenotypic, imported in the XNAT databasing system. To install and use this release you should go through the documentation provided below.

INDI-Lite

This release includes all data, both imaging and phenotypic, but does not include the XNAT database. INDI-Lite is structured as follows:

  • subject-ID
    • scan session ID (some subject might have more sessions)
      • DICOM: this folder contains dicom images for each scan
      • NIFTI: this folder contains nifti images for each scan
      • Phenotypic: this folder contains a csv file that contains all phenotypic data for that particular subject.

Setup

System requirements

  • Virtual box (works on Windows, MAC OSX and Linux)
  • At least 30GB of free space for the INDI installation plus additional free space for any data that you add (Keep in mind that this might grow quickly!)

Getting Started

  • Download the appropriate version of Virtual Box from the following website and install it on your computer. Download Virtual Box Here
  • Unzip the INDI Virtual Machine (tar -xzf VM.000.006.tgz). Be sure to do this a in folder that will suit your project (e.g. /home/me/INDI) and be aware that this folder will grow considerably as you add data. After unzipping you should see a file called: INDI.vdi and a folder called xnat. This is a shared folder between your computer and the virtual machine that contains the configuration files for xnat
  • Create a folder on your computer that can function as a folder that can share information/documents/files between your computer and the Virtual Machine. e.g., /home/me/INDI/host. It is IMPORTANT that this folder is called host. If you do not setup this folder correctly you will see an error message when you start the virtual machine.

Installing Virtual Box and Loading the INDI Hard Disk

  1. Start Virtual Box and click New at the upper left corner
  2. Click Continue at the lower right corner
  3. Enter "INDI" in the Name field
  4. Select Linux from the Operating System drop-down menu
  5. Select Ubuntu from the Version drop-down menu
  6. Select 1024MB for the amount of base memory allocated to the virtual machine
  7. Select the Virtual Hard Disk by selecting "Use Existing Disk" and pressing the folder icon next to the drop-down menu. Click "Add" at the upper left corner and navigate to INDI.vdi (this is you INDI virtual machine). Highlight INDI.vdi and click Select.
  8. Click Done
  9. Please Note: 100GB is the maximum disk space allocated to the Virtual Box; it will not actually use that much space on your hard-drive

Using Your INDI Virtual Machine

Working with your INDI Virtual Machine

  1. Start Virtual Box by double-clicking on the icon. You should see your INDI virtual machine in the left panel.
  2. Click Settings on the upper left corner
  3. Go to the Shared Folders tab
  4. Click on the tiny folder icon with a green plus sign on it on the right side. An Add Share window should open.
  5. Select "Other" from the Folder Path drop-down menu and select the xnat folder that came with your VM download. Click Choose. It should appear in the Add Share window. Make sure it is called "xnat" and hit Ok. It should now appear in the Shared Folders window.
  6. AGAIN click on the tiny folder icon with a green plus sign on it on the right side. An Add Share window should open.
  7. Select "Other" from the Folder Path drop-down menu and select the host folder you created. Click Choose. It should appear in the Add Share window. Make sure it is called host and hit Ok. It should now appear in the Shared Folders window.
  8. Power on your virtual machine by double-clicking on "INDI" in the left panel.
  9. You should see Ubuntu boot on your computer
  10. Please Note: The virtual machine is set up for automatic log-in, but if necessary or if you want to change this, the username is "INDI" and the password is "indi".
  11. Double-Click the INDI link in the middle of the screen to launch XNAT with the INDI database
  12. You are ready to browse and examine the different projects and datasets!

Stopping your INDI Virtual Machine

You have to power down the virtual machine like a normal computer. You should NOT just close the window. This is very important because your database or virtual machine might get corrupted if you do not power down correctly.

To power down the virtual machine properly, do the following:

  1. Close XNAT
  2. Go to System -- Shut Down

Adding data to your INDI release (Start from scratch or adding weekly releases)

These steps explain how you can add data to your local copy of INDI. The steps are similar whether you start from scratch or are updating your copy of INDI with the weekly added releases.

INDI-Lite

After downloading and uncompressing a release (e.g. tar -xzvf NKI.006.001.tar.gz), you can just move the new subjects to your main INDI folder (e.g., /home/me/INDI/). The subject numbers are unique so older datasets will not be overwritten.

INDI-XNAT

  • Download a DICOM or NIFTI release (whichever you prefer). See here for these files. Place the file you downloaded in the host folder. NOTE: you can do this either from your actual computer or from within the Virtual Machine. In both cases it is important that you place the downloaded file in the host folder.
  • Unzip the file you just downloaded (e.g., tar -xf NKI.archive.1-5.NIFTI.tar). After unzipping you should see a folder that has the name of the release (e.g., NKI.archive.1-5.NIFTI).
  • If you are not already there: Start the Virtual Machine
    • All commands and actions below are done in the Virual Machine
  • Open a terminal and navigate the the host folder
    • cd ~/Desktop/host
  • If you haven't uncompressed the INDI XNAT dataset you downloaded, now is a good time to do so (e.g. tar -xzvf NKI.006.001.DICOM.tar.gz). Upon completion you will see a folder with the name of the release.
  • Navigate to ~/Desktop/scripts
    • cd ~/Desktop/scripts
  • In that folder is a script called 'uploadXmlToXNAT.pl'. This script will update your XNAT database by adding the datasets and phenotypic information.
  • Run the script to update your release by typing:
    • ./uploadXmlToXNAT.pl ~/Desktop/host/NKI.006.001.DICOM
      or
    • ./uploadXmlToXNAT.pl ~/Desktop/host/NKI.006.001.NIFTI
    • Replace NKI.006.001 as needed depending on the name of the release.
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