OMR CRF Import

The OMR-CRF is a questionnaire that is generated using the SDAPS software to enable Optical Mark Recognition. To process filled CRFs and import their data into XNAT, we have developed a tool that automates the different stages as much as possible.

The CRF import functionality is available at the DDI Tools portal at http://p96-podman:8181, to access it, navigate to that address in the web browser and select "Import" item on the left navigation panel. Import overview

ℹ️ The CRF import tool is compatible with CRF versions 4.6.0 and greater. Previous versions cannot be processed to extract the data and can only upload the associated scans with the CRF Split & Upload tool.

How to import OMR CRFs into XNAT

To import the CRF data and scanned documents into XNAT you need to follow a series of steps:

  • Scanning the CRF.
  • Import the scan file into TSD.
  • Navigate to the import tool.
  • Provide the subject and visit data.
  • Select the file uploaded in TSD for processing.

Scanning the CRF

SDAPS need a specific TIFF format file for it to process the optical mark recognition. The scanner must be set to 300 DPI black and white, multipage TIFF, compressed.

⚠️ THE ORDER AND NUMBER OF PAGES CANNOT BE ALTERED. SDAPS keeps a record of where the check marks are placed and expects the logical ordering. The pages from extra documents may be added after the CRF.

Uploading the scan file into TSD

See the TSD import user guide for importing files in case of any doubts.

Importing the CRF with the Import tool

Once you have the scan available in TSD, use the Firefox browser to navigate to http://p96-podman:8181 and click on the Import item on the left navigation panel.

XNAT login

The tool will then ask for your XNAT credentials so it can import the recognized data and upload the documents into XNAT. Provide your username and password and hit enter. If the credentials are correct the app will ask for the details about the CRF vist.

CRF visit details

  1. Project: Select the desired XNAT project from the dropdown list.
  2. Subject: Type in the subject identifier.
  3. Visit Date: Use the calendar tool to select the date of the assessment visit.
  4. Assessment Visit: Pick the type of assessment visit from the dropdown menu.

Form Fields

You can modify these items at anytime, hit enter to apply the changes.

CRF scan upload

With the visit details, the app will show the file input for you to upload the scan file. Click on the "Browse files" button to choose a scanned CRF document in TIFF format. The app will show a preview of the first page of the CRF and the detected page count.

CRF

Process and review

You can now click on the Process button to start importing the CRF. The app will create the experiments and set their fields with the recognized marks from the CRF, and then split the different documents identified by QR codes and upload them into XNAT.

The app will provide feedback about the different steps and progress.

CRF

Once it finishes, the app will provide a direct link to the subject to which the data was imported. OMR software is not infallible; SDAPS can make mistakes when deciding whether a checkbox is checked. Also, sometimes the person may have made a mistake when filling out the questionnaire. Therefore, it is very important to inspect the resulting data in XNAT that was set from the import process.

CRF