Difference between revisions of "Image submission plug-in"

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== About MIPAV Imaging tool==
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== MIPAV Image Submission plug-in ==
  
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One can upload unprocessed brain images in [[Other formats supported by MIPAV#DicomFormat|DICOM format]] to FITBIR. FITBIR also supports processed images in a variety of formats including DICOM, MINC 1.0 and 2.0, Analyze, NIfTI-1, AFNI and SPM. If you are using a different file format, please contact FITBIR-help@mail.nih.gov to allow us add it to our list of supported standards.
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One can upload unprocessed brain images in [[Other formats supported by MIPAV#DicomFormat|DICOM format]] to [http://fitbir-demo.cit.nih.gov/ FITBIR]. [http://fitbir-demo.cit.nih.gov/ FITBIR] also supports processed images in a variety of formats including DICOM, MINC 1.0 and 2.0, Analyze, NIfTI-1, AFNI and SPM. If you are using a different file format, please contact FITBIR-help@mail.nih.gov to allow us add it to our list of supported standards.
  
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To submit imaging data to FITBIR, researchers are required to run a component of the MIPAV (Medical Image Processing, Analysis, and Visualization) application. Using the MIPAV Component for FITBIR, you can quickly prepare your image data for submission by following the steps below.
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To submit imaging data to [http://fitbir-demo.cit.nih.gov/ FITBIR], researchers are required to run the Image Submission plug-in. Using the Image Submission plug-in, one can quickly prepare the imaging data for submission by following the instruction provided on this page.
  
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    Place each of your images into a common directory accessible by your computer.
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=== System requirements ==
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    Select the link: http://mipav.cit.nih.gov/fitbir_jws/mipav_fitbir_prod_jws.php. This link will launch a java web start application. A recent version of the Java Runtime Environment (JRE) is needed to run the application.
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    Add Files to the program.
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A recent version of the Java Runtime Environment (JRE) is needed to run the plug-in.
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    Enter appropriate metadata. 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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    Add or Remove files, select the output directory, and select finish when all files have the meta data items completed.
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=== Run Image Submission plug-in ==
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    Select Finish, which will generate all the files necessary for validation
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* Add Files to the program.
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        The compressed image
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* Enter appropriate metadata. 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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        A JPG that can be used as a thumbnail to preview the image in the FITBIR query tool
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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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        A CSV of the meta-data from the image. The data matches a form structure that is queryable in FITBIR's query tool.
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* Select Finish, which will generate all the files necessary for validation
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    Validate the files in the FITBIR Validation Tool.
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** The compressed image
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** A JPG that can be used as a thumbnail to preview the image in the FITBIR query tool
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** A CSV of the meta-data from the image. The data matches a form structure that is queryable in FITBIR's query tool.
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*Validate the files in the FITBIR Validation Tool.
  
 
[[Category:Help]]
 
[[Category:Help]]
 
[[Category:Help:Stub]]
 
[[Category:Help:Stub]]
 
[[Category:Help:Algorithms]]
 
[[Category:Help:Algorithms]]

Revision as of 16:32, 21 June 2013

This page is a stub.

The Image Submission plug-in is used to submit imaging data to the Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system.

About FITBIR

The Federal Interagency Traumatic Brain Injury Research (FITBIR) informatics system was developed to share data across the entire Traumatic Brain Injury (TBI) research field and to facilitate collaboration between laboratories, as well as inter connectivity with other informatics platforms. This community-wide sharing requires using common data definitions and standards, as well as comprehensive and coherent informatics approaches.

To learn more about FITBIR, please refer to the FITBIR Frequently Asked Questions page.

To access FITBIR Demo,use this link.

To download FITBIR Submission request in PDF, use this link


MIPAV Image Submission plug-in

One can upload unprocessed brain images in DICOM format to FITBIR. FITBIR also supports processed images in a variety of formats including DICOM, MINC 1.0 and 2.0, Analyze, NIfTI-1, AFNI and SPM. If you are using a different file format, please contact FITBIR-help@mail.nih.gov to allow us add it to our list of supported standards.

To submit imaging data to FITBIR, researchers are required to run the Image Submission plug-in. Using the Image Submission plug-in, one can quickly prepare the imaging data for submission by following the instruction provided on this page.

= System requirements

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

= Run Image Submission plug-in

  • Add Files to the program.
  • Enter appropriate metadata. 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.
  • Add or Remove files, select the output directory, and select finish when all files have the meta data items completed.
  • Select Finish, which will generate all the files necessary for validation
    • 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 the FITBIR Validation Tool.
Retrieved from "http://mipav.cit.nih.gov/pubwiki/index.php?title=Image_submission_plug-in&oldid=46803"