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The XNAT Upload Assistant tool is a standalone Java application purpose-built to anonymize and upload image session data





to CNDA. This tool contains the same core functionality as the upload applet, which is no longer being supported by web browsers.

Downloading


The XNAT Upload Assistant application requires that Java 1.7 (or higher) be installed on your computer. Java can be downloaded from here: http://www.java.com.

You can download the XNAT Upload Assistant from https://download.xnat.org/upload-assistant. You will be able to choose the specific download for the type of operating system you are using. If you are unsure of which version to download, please contact your IT department to confirm your operating system version.

Installing

When you click the "Download..." link, depending on the browser you are using, you may receive an option to run the executable right away. If so, then click Run.

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Please click Yes or OK for any additional pop-ups that may occur. Example: "Do you want to allow the following programs to make changes to this computer?”

If you do not receive the Run option immediately, then please follow the menus to save the installer file to your computer. You can save this file into a temporary directory because you won't need it again after installation is complete.
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Once you have saved the Upload Assistant installer file, you can navigate to the executable file through your browser's download list(usually located in the top right hand corner of your browser window).

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Click once on the download list icon in your browser. Then click once on the link for the uploader-assistant.exe file(exact name may vary slightly). This should launch the installation of the Upload Assistant. Follow the instructions above, clicking Run, Yes, or OK as necessary until the install wizard is launched.

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The wizard will walk you through the rest of the steps to install the Upload application. After the screen above, please click Next to continue. The installer will select a default location to install the software but you may change the location if you wish, by clicking Browse. If the default location is acceptable, please click Next to continue.

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Next, you will be asked whether or not you would like to add shortcuts for this application. Please select your preference or just accept the defaults by clicking Next.
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Upon successful completion of installation, you will see the following screen. Click Finish to run the Upload Assistant for the first time.

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Running the Upload Assistant for the First Time


The first time the Upload Assistant opens, you will need to enter some information into the tool. This information will be saved so that when you open the tool in the future, you won’t need to complete this step again.

Please enter the following values:

Server Address: cnda.wustl.edu
Allow unverified certificates: unchecked
Username: your CNDA user id

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Click Save to store these values, then click Next to continue. If you wish to continue uploading images, please skip down to the Uploading Images section. Otherwise, select cancel to exit the application; your settings will be saved.

Uploading images


If the Upload Assistant is not already running, launch it from the shortcut created during installation. In Windows, this would mean navigating to: Start>All Programs>XNAT Upload Assistant>xnat-assistant. The program should launch with the previously saved settings.

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Log in
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Select your project and then click Next.
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Click the subject to upload to or to make a new subject click on the create new subject button on the right hand side.
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    • To create a subject, enter subject label and click Create.
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Click Next.

Enter session date, or click I don’t know. Choosing either option is fine.
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Click Next.

Select the directory where the files are stored.
    • NOTE: Files can be uploaded from a CD but it is usually best to copy them to the local machine and upload from there.
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Click Next.

Review the series you are uploading and confirm they are correct by clicking Next.UsingUploadAsst9.jpg
The last screen before uploading will suggest a name for the session being uploaded, but this can be changed to whatever you would like. This name just needs to be a unique ID.
    • NOTE: Be aware of any project specific naming protocols that may be in use.UsingUploadAsst10.jpg


























Upon upload completion, you can click the link Click here to finish archiving the data to enter in additional image session details or you can click Close.
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If you click Click here to finish archiving the data you will be redirected to cnda.wustl.edu. Log into CNDA if prompted.

The session information page will display when finished. The data will be organized according to the CNDA IDs that you have just entered.

When the session is done archiving, you will receive an email notice like this one:

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Entering Additional Image Session Details


To enter additional session details, log into CNDA via a web browser at https://cnda.wustl.edu. Once you have logged in, you will see the session you just uploaded listed in the Recent Data Activity section. Click the session label to go to the session page.
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To edit the session, go the Actions box in the top right hand corner and click the Edit link.

For each scan, enter all metadata and any notes that have been written on the Scan Information Sheet in the notes section provided.

To enter notes, go to the session information page, click the Edit link in the Actions box on the right.
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In the Additional Notes section of the Modify Session page, enter any notes from the Scan Information Log that are applicable for the entire imaging session.
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Click the Submit button.