Beginner's Guide to Shanoir

Shanoir-NG is a web app and a desktop client that helps imaging researchers, radiologists, radiographers and MRI operators to collect, organize, archive and share imaging data.

Login

To access Shanoir you will need a Shanoir account. You can either :

• Ask for an access to a public study on the Shanoir Welcome page.
• Create a new account on the "Sign In" page.
• Ask for a colleague who has administration rights on a study to add you as a study member with your email in the Study menu.

Add a new user to a study

As a study administrator, you can add other users to your study, whether they already have a shanoir account or not. Here is how to do that:

• Open the details of your study
• Go to the "Member" tab and click edit:

You can enter the email address of someone, shanoir will send an email to create an account (if it doesn't already exist). If the email is already known by shanoir, the user will be added to that study.

Main Features

All Shanoir features are available on the left menu :

• Dataset search : search for data already imported in Shanoir database

• Medical Data : access and manage your studies, subjects examinations and imaging acquisitions

• Medical configuration : create acquisition centers and their equipment, create fine mappers and data filters for your study (study and quality cards)

• Preclinical : manage your preclinical studies

• Import data : import imaging data to your study (DICOM, BIDS, Bruker, EEG, processed)

Import data

Here is an example of a DICOM zip directory imported into Shanoir :

**Step 1/3 : Select a DICOM archive and load it into Shanoir **

If you plan on importing multiple examinations at once, please check "Multiple examination import" (1) and follow the recommandations. If a DICOMDIR is present, it will be used to import the data. If not, a DICOMDIR will be automatically generated from the DICOM instances present at the root of the archive.

By clicking "Choose file" you'll browse your local volumes to choose the DICOM archive to import (Shanoir accepts only archives when importing in DICOM). (2)

Then Shanoir will load your archive and display it in green if it is OK or red if it wasn't readable.

If OK, you'll be able to see the DICOM modality type of your chosen examination. (3)

Click "Next".

Step 2/3 : Select the specific DICOM serie that you want to import

Select by checking it the whole examination (corresponding to the patient in bed icon) or the specific acquisition (with the brain icon) that you wish to import. (4)

You can preview informations about your selection and the acquisition itself by clicking on the eye icon. (5) In the preview viewer :

• / - allow you to go to the next/previous slice “Swap view” change the axis of the acquisition Use “Go to center” / “Go to Origin” to place the cursor automatically.

If OK, click on "Next"

Step 3/3 : Set the clinical context

Select the Study where you want to import your DICOM data. (6) Shanoir will only display the studies you have access to. You can inspect the study informations by clicking on the eye icon.

Select a Study card. (7) Study cards are specific to a study and an acquisition center linked to the study and allow to set specific values to Shanoir entities and DICOM attributes based on the values of the imported data. Well used, Study cards allow DICOM data from various centers and machines to be homogenized within a study with proper metadata.

"Acquisition Center" and "Center equipment" fields display the center and the machine the selected study card is linked to. If the study card selected is not compatible with the center or the machine of your DICOM files, a message like below will be displayed but you'll be able to import nonetheless.

You can either create a new subject (8) or select an existing one in your study (9).

You can also create a new examination or select an existing one if DICOM data with the same StudyInstanceUID was already imported in your study. (10)

To be able to click on "Import now" you have to select a study, a study card, a subject, a subject type and an examination.

See the status of your import in the "Jobs" menu

During the import you are able to see the progress of it on the left menu under the "Jobs" title. (11) By clicking on the "Jobs" menu you'll have the details about the running job. When finished you'll be able to go to your newly imported examination by clicking the icon in the "Message" column. (12)

Create Subject

Last Name, first name and birth date come from DICOM metadata. (13)

If the DICOM data was already anonymized : the field “Common name” will take the "Patient Name" value coming from the DICOM metadata. In case the subject is not already anonymized : during import, Shanoir will pseudonymize the DICOM data following recommandation of the DICOM standard. For more informations on the subject please read our pseudonymization page.

A global identifier for the subject will automatically be generated using the first name, last name and birthdate. This could help identifying a subject that was already imported in the database (in another study).

Use the field “Common name” to put the subject code in the study. (14)

Fields with a * are mandatory.

Dataset search

By clicking on the "Dataset search (Solr)" of the left menu you can search datasets based on one or multiple criteria and visualize, download, delete or process them on the VIP platform.

You can use the filters on the left to filter the results on one or multiple criteria. (15)

By activating the toggle "Expert mode" you can use the text field above to enter a Solr query to filter results. (16)

You can select with the tick boxes several datasets of interests and apply to them all the features described above the table (Clear selection, Delete selection, Apply Study card, Run a Process...). (17)

For each dataset (line in the table) you can click on the icon in the "View Dicom" column and view the DICOM acquisition. (18) This will open OHIF viewer and allow you to use all the OHIF features on this dataset, including segmentation, 3D reconstruction...

Report a Bug

You can report a bug on this repository Add a title and a comment concerning the issue with as much details as possible and the way to reproduce the issue, and click "Submit new issue".