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Advanced data import configuration§

This page is for UCL members who manage projects on the UCL XNAT servers maintained by the MIRSG team.

These options support more advanced XNAT workflow relating to how data are imported and stored. In most cases you do not need to modify these settings.

We recommend you do not change these settings unless you understand the implications to your project.

Create a custom resource uploader for uploading non-DICOM files§

If your users regularly need to upload non-DICOM files, you may wish to create a custom resource uploader. This simplifies the upload procedure by defining in advance how the data files should be stored.

Enable the data quarantine§

If you enable the quarantine, then any data you upload will be held in an inactive (quarantine) state until you click the Activate link for that data on the XNAT server. While inactive, the data cannot be shared or used in processing. This could be useful if you wish to review data before permitting it to be used in automated processing pipelines.

We do not support using the quarantine to verify anonymisation. PII must be removed before data are uploaded to the server, so any verification checks must be done before you upload the data.

To enable the quarantine for your project:

  • Log into the XNAT server
  • Navigate to your project (Click the Browse drop-down, click My Projects and select your project)
  • Select the Manage tab.
  • Select Define Quarantine Settings
  • Select YES
  • Click Save

Enable the data prearchive§

If you enable the prearchive, then any data you upload will not go straight into your project but will be placed in the temporary prearchive. You can review data in the prearchive before choosing to archive it in your project or rejecting and deleting.

We do not recommend enabling the prearchive unless you have a specific need, as it is shared across the server and could allow other users outside your project to access your data and accidentally assign it to their project. If you need to examine and approve data before adding to your project, we recommend you do this on-site before upload.

We do not support using the prearchive to verify anonymisation. PII must be removed before data are uploaded to the server, so any verification checks must be done before you upload the data.

To enable the prearchive for your project:

  • Log into the XNAT server
  • Navigate to your project (Click the Browse drop-down, click My Projects and select your project)
  • Select the Manage tab.
  • Select Define Prearchive Settings
  • Select All image data should be placed in a temporary location (prearchive) before being manually transferred into the permanent archive.
  • Click Save

See the prearchive documentation for how to use the prearchive.

Permit overwriting of files during upload§

If you upload images whose DICOM identifiers match existing images in your project, the upload will normally be rejected. You can instead permit the upload to overwrite the matching files. This can lead to loss of data if your files have the wrong DICOM metadata.

  • Log into the XNAT server
  • Navigate to your project (Click the Browse drop-down, click My Projects and select your project)
  • Select the Manage tab.
  • Select Define Prearchive Settings
  • To permit overwriting of files:
  • Select the third option: All image data will be placed into the archive automatically and will overwrite existing files. Data which doesn't match a pre-existing project will be placed in an 'Unassigned' project.
  • To prevent overwriting of files:
  • Select the second option: All image data will be placed into the archive automatically, but anything matching existing files will be rejected. Data which doesn't match a pre-existing project will be placed in an 'Unassigned' project.
  • Click Save

Enable series import filters§

You can add series import filters to restrict which images can be uploaded to your project. Series import filters are matched against the DICOM series description. If they match, the series upload is either permitted (whitelist) or prevented (blacklist). Series import filters can be useful if your users will regularly be uploading selections of image data where there are certain types of series you don't want to store, but where it is hard for the user to filter these out before upload.

Series import filters generally have to be custom written for your project, because the DICOM series description is not standardised and depends on your data. Series import filters may not be flexible enough to cover all cases where you want to filter data. If you are developing an automated upload procedure, you may prefer to filter the images in your upload code, as this will give you more fine grained control.

To set or modify series import filters:

  • Log into the XNAT server
  • Navigate to your project (Click the Browse drop-down, click My Projects and select your project)
  • Select the Manage tab.
  • Select Series import filters
  • Check Enable Filter
  • Select Whitelist or Blacklist as appropriate and follow the instructions Setting Project-specific Series Import Filters in the XNAT documentation.

Warning: if you use series import filters to filter out datasets containing personal identifiable information (PII), you must only use upload methods that apply filters before upload (such as the XNAT Desktop application). Other methods (such as compressed file upload or DICOM receiver) only apply filters after the data has been received by the servers, but you must not send data containing PII to the XNAT servers.

Enable modality map§

A modality map allows your project to set the modality of new sessions based on DICOM information in the incoming data. It cannot be used alongside a series import filter.

To set or a modify modality map:

  • Log into the XNAT server
  • Navigate to your project (Click the Browse drop-down, click My Projects and select your project)
  • Select the Manage tab.
  • Select Series import filters
  • Check Enable Filter
  • Select Modality mapand follow the instructions Setting Project-specific Series Import Filters in the XNAT documentation.

Clean up the scan type labels§

When you import DICOM data, XNAT automatically labels it with a scan type based on the series description.

You may end up with multiple different scan type labels which really refer to the same type of scan. This can happen because series descriptions are not always consistent between scans, for example due to differences between operators or scanning equipment.

You can fix this using the Scan Type Cleanup option which is available from from your project home

  • Navigate to your project home:
  • From the menu bar, select Browse -> My Projects -> (your project name)
  • From the Actions menu at the right, click Scan Type Cleanup
  • A list is shown of the scan types in your project. Each row shows one mapping, which shows the Scan Type label that is assigned to the scans matching the DICOM metadata shown in that row
  • To change the mapping for a row, enable the checkbox and modify the Scan Type to your desired scan type label
  • Click Submit when complete.

See Cleaning Up Scan Types In Your Project for more information.