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User Guide

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Laurent Paul Vallet edited this page Jun 10, 2024 · 6 revisions

A French version is available here.

Shanoir Uploader allows you to query a PACS (or a local file system folder) and select examinations to import into the Shanoir database as new elements of a clinical study.

The Shanoir web interface then allows you to administer this study and explore its content.

Installation

The installation process is detailed in this wiki.

Use

Profile choice and authentication

If your network configuration allows access to the URL of the Shanoir web interface, then the application will ask you to choose a profile:

login

The choice of profile depends on your study of interest and the Shanoir environment to which you wish to import your DICOM exams.

You are asked to save the profile chosen in the application configuration.

The profile is saved in the basic.properties file (created in a ~/.su_v8.0.0/ directory for the version 8.0), you can reset this choice at any time or modify it with the 'profile' parameter in your basic.properties file.

If the Shanoir server is accessible and a profile is entered, Shanoir Uploader displays an authentication page.

Use your Shanoir username and password. If you do not have a Shanoir user account, you can request one via the Shanoir web interface for Neurinfo or for OFSEP. Depending on your profile "Neurinfo" (shanoir.irisa.fr) or "OFSEP" (shanoir-ofsep.irisa.fr) orient yourself to the matching server URL.

Importing DICOM data

From a PACS

Querying a PACS for DICOM data and importing it into Shanoir server is the main feature of Shanoir Uploader and is done using the two main tabs of the app.

1st step - Locally prepare data

The first tab allows you to query a PACS using the following fields :

  • Name of the patient
  • ID of the patient (equals IPP)
  • Birth Date
  • Description of the study
  • Date of the study
  • Modality of the DICOM data

queryPACS

The field "Patient Name" can be filled using the "*" wildcard character (click on the "Help" button for detailed informations).

On some PACS (e.g Telemis), querying using the date of the study or its description works when the patient's name does not return any results.

Once you selected your data of interest you'll have to verify patient's informations before clicking on the "Download (PACS) or copy (CD/DVD)" button

verifyData

You can modify any of the fields, the Birth Name and Birth Date fields are mandatory to import data.

Once you click on "Download (PACS) or copy (CD/DVD)" a pop-up window will tell you that you can import your data in the server with the 2nd tab.

You can select and verify as many DICOM data as desired before going on with the 2nd tab.

2nd step - Import data into Shanoir server

The 2nd tab allows you to select multiple informations in order to import the DICOM data in the right Shanoir study, applying the right study card, selecting the center and setting a specific Shanoir patient's name if desired.

importData

From a directory containing DICOM files

importDcmFile

  • Only folders (and not .zip archives) can be selected from the "Open DICOM files..." menu.

  • A “birth name” (in the absence of study-related directives, can be a copy of the name) as well as a date of birth must be provided in order to be able to import the DICOM.

  • The import menu then allows you to select the study, the patient, the study card and the center already associated with the study in Shanoir.

From a .csv file (mass import)

You can import multiple datasets at once from a PACS using a configured CSV file. This feature is detailed on this page.

Import a whole study from a directory

Shanoir Uploader allows you to import a whole study into Shanoir or a part of this study. Your folder containing the study must be unzipped and following the Brain Imaging Data Structure standards.

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