Difference between revisions of "Image submission plug-in"

Revision as of 13:44, 11 July 2013

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3. General info

Introduction

The Image Submission Package Creation tool, which is available via MIPAV Image Submission plug-in is used to submit imaging data to - the BRICS data dictionary.

Uploading imaging data to the BRICS data dictionary

TBD.

Write a short outline that explains how to upload data to the BRICS data dictionary. Explain why do we need to create the submission package and why use the Validation tool.

MIPAV Image Submission plug-in

MIPAV Image Submission plug-in is designed to help researches to upload the image submission package into the BRICS database. The image submission package includes the brain image file and the queryable meta data that describe the image.

Supported image formats

The plug-in supports all file formats supported by MIPAV including processed and unprocessed brain images in DICOM format. If you are using different file format (not supported by MIPAV), please contact MIPAV support.

System requirements

A recent version of Java Runtime Environment (JRE) is required to run the plug-in.

Running the Image Submission plug-in

The Image Submission Package Creating plug-in - the main window unpopulated with data

Using the form structure

1. Run the Image Submission Package Creation tool. To run the plug-in form MIPAV, go to Plug-ins> Generic> FITBIR Image.
2. The main plug-in window appears.
3. In the main window, use the corresponding buttons to add the image file(s) and metadata files, such as a CSV file and the form structure that are needed in order to create the submission package.
4. To upload the form structure from the data dictionary, use the Add Form Structure button. The Choose Form Structure window appears displaying the form structures available from the BRICS data dictionary. Select the form structure and press Add.
5. The Edit Data Elements window appears populated with the data elements from the selected form structure.
6. If you use DICOM files, navigate to the Imaging File Name field and use the Browse button to select the file.
7. The information from the DICOM header will be automatically populated into the Edit Date Elements window.
8. Review the information entered in the previous step. Make sure that all required fields are filled in. The required fields appear in red. If some of required fields are empty, the form structure status will appear as not completed and the submission package might fail validation.
9. Manually enter the missing image information.
10. In order to complete the submission package, the following information needs to be entered into the Edit Data Elements window: i) the patient/subject information including GUID, a patient/subject age, a study site name, and a visit date and ii) the image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality. See also Required image information.
11. After all required fields have been filled in, press Save.
12. Select the output directory which would be used by the Validation tool to store temporary files and validation logs.
13. Press Generate Files. This will generate the submission package.

Using a CSV file

1. To upload a CSV file, use the Load CSV File button.

TBD.

Notes

• If the Image Submission plug-in does not appear in the menu, you might need to install the plug-in. If the installed plug-in did not appear in the MIPAV menu under Plug-ins> Generic, restart MIPAV.
• Depending on the form structure required data may vary. Refer to Required image information for more information.