Difference between revisions of "Image submission plug-in"

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This page is a stub.
 
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The Image Submission Package Creation tool which is available via MIPAV Image Submission [[Understanding plug-in programs][plug-in]] is used to submit imaging data to - the BRICS Data Dictionary.
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The Image Submission Package Creation tool which is available via MIPAV Image Submission [[Understanding plug-in programs|plug-in]] is used to submit imaging data to - the BRICS Data Dictionary.
  
 
== MIPAV Image Submission plug-in ==
 
== MIPAV Image Submission plug-in ==
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'''Note:''' If the Image Submission plug-in does not appear in the menu, you might need to [[Installing a plug-in|install the plug-in]]. If the installed plug-in did not appear in the MIPAV menu under '''Plug-ins> Generic''', restart MIPAV.
 
'''Note:''' If the Image Submission plug-in does not appear in the menu, you might need to [[Installing a plug-in|install the plug-in]]. If the installed plug-in did not appear in the MIPAV menu under '''Plug-ins> Generic''', restart MIPAV.
 
# The main plug-in window appears.  
 
# The main plug-in window appears.  
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# Use the main window to add the image file(s) and appropriate metadata that form the submission package.
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# In the main window, use the corresponding buttons to add the image file(s) and appropriate metadata that form the submission package.
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# Metadata can be entered manually, as a form structure or uploaded as an CSV file.
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# Enter metadata. Metadata can be uploaded as a form structure or as an CSV file.
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## To upload the form structure use the Add Form Structure button.
 
## To upload an CSV file, use the Load CSV File button.
 
## To upload an CSV file, use the Load CSV File button.
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# Enter the required image information (required data are shown in red) including:
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* Enter appropriate metadata including Age in months, date of interview, extent, GUID, Dimensions, and site subject ID are all required. You may need to scroll down to access all required fields.
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## The patient/subject information - GUID, a patient/subject age, a study site name, and a visit date;
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* Add or Remove files, select the output directory, and select finish when all files have the meta data items completed.
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## Image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality.
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* Select Finish, which will generate all the files necessary for validation
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'''Note:''' Depending on the form structure required data may vary. However, the following data are always required - GUID, a patient/subject age, a study site name, and a visit date.
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# Select the output directory which would be used by the Validation tool to store temporary files and validation logs.
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# When all metadata and image files are selected, press Generate Files.  This will generate the submission package.
  
 
** The compressed image
 
** The compressed image

Revision as of 13:28, 24 June 2013

This page is a stub.

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.

MIPAV Image Submission plug-in

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

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

  1. Run the Image Submission Package Creation tool. To run the plug-in form MIPAV, go to Plug-ins> Generic> FITBIR Image.

Note: 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.

  1. The main plug-in window appears.
  2. In the main window, use the corresponding buttons to add the image file(s) and appropriate metadata that form the submission package.
  3. Enter metadata. Metadata can be uploaded as a form structure or as an CSV file.
    1. To upload the form structure use the Add Form Structure button.
    2. To upload an CSV file, use the Load CSV File button.
  4. Enter the required image information (required data are shown in red) including:
    1. The patient/subject information - GUID, a patient/subject age, a study site name, and a visit date;
    2. Image information including - imaging study date and time, imaging file name, imaging file itself, imaging file format and modality.

Note: Depending on the form structure required data may vary. However, the following data are always required - GUID, a patient/subject age, a study site name, and a visit date.

  1. Select the output directory which would be used by the Validation tool to store temporary files and validation logs.
  2. When all metadata and image files are selected, press Generate Files. This will generate the submission package.
    • The compressed image
    • A JPG that can be used as a thumbnail to preview the image in the FITBIR query tool
    • A CSV of the meta-data from the image. The data matches a form structure that is queryable in FITBIR's query tool.
  • Validate the files in using Validation Tool.
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