Center For Advanced Molecular Imaging

Data Management

Exporting data from the 7T MRI

You can find a pdf file with screenshots of key operations here.

  1. Export your data from Paravision
    1. Close Exam card.
    2. Locate and select study in Data Browser window.
    3. Click “Export DICOM” and save into the default folder.
    4. Use menu next to “Export DICOM” button to select “Archive”.
    5. Go to computer’s file browser and find your exported data in the /home/nmrsu/tmpdata and /home/nmrsu/tmpDICOM directories.
    6. For exported raw data, change the extension from .PvDatasets to .zip
    7. For the DICOM directory, right-click, “create archive”, and make a .zip or .tar.gz file.
  2. Transfer your data to the CAMI workstation using Box
    1. Open web browser and log into Northwestern Box.
    2. Use the upload file menu in Box to upload your zipped archive and DICOMs.
    3. After successful upload, delete your archives from the temporary folders on the 7T workstation.
    4. Go to CAMI workstation in the lobby.
    5. Log in and start a NUCore reservation.
    6. Download your .zip archive from Box to your data folder on the workstation (NOT the desktop!) and unzip it.
  3. Start JIM and convert your raw data into a usable image format (.nii)
    1. Log into NU VPN using the Windows network button.
    2. Start JIM software.
    3. Open Image conversion tool, navigate to your image storage directory, press “Scan for images” button.
    4. Set image export directory.
    5. Select desired images and press “convert”
  4. For quick viewing without conversion, you can load the DICOM files as stacks in ImageJ. Note that you will usually need to adjust the image contrast.
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