User's Guide

Introduction

The purpose of the Shanoir project (standing for Sharing NeurOImaging Resources) is providing a platform to share neuroimaging data.

Shanoir offers users to manage, import and retrieve data from medical imaging devices. A lot of modalities are available.

To specify neuroimaging data to be imported, users are asked to give related meta-data which are structured according to an ontology (OntoNeuroLOG).

Enhancing the workability of the data while maintaining their integrity, Shanoir allows Researchers, Clinicians and Engineers to undertake quality research projects with an emphasis on distant collaboration.

Furthermore, Shanoir makes easier data retrieval from the database through the possibility to search for records according to the associated meta-data.

Shanoir is a web-based solution, developed from the web application framework JBoss Seam and therefore doesn't need any client installed on your local machine.

Shanoir is a project carried out by the VisAGeS Team, based at IRISA (INRIA Rennes - Bretagne Atlantique Research Centre).

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Copyright

Shanoir is INRIA 2009 copyrighted.

Overall

Les rôles utilisateur

Manage Data

Create/Update/Delete Entities

Retrieve datasets

Import Data

The Data Import feature offers to bring data in Shanoir. This data are neuroimaging records. At this stage, MRI is the only supported modality. Imported data can be raw data (i.e. directly produced by the MRI devices) or processed data (i.e. data resulting from applied filters and algorithms, ex: noise reduction). It is also possible to import spectroscopy data and so on …

Raw Data Import Feature

Whatever the data source (CD/DVD, DICOM associations, files), the process is always the same and is explained by the following steps:

  1. Choose the Import type: the user has to choose the data source type.
  2. Select Data: this step may vary depending on the Import type.
  3. Select Modality: at this stage, only MRI is supported.
  4. Select Clinical Context: select or create a clinical subject, study, examination centre …
  5. Process Data Anonymity: ascertain the “namelessness” of the data to make that no private patient details are to be found in the database. It is also possible to backup the data on a PACS. Images are converted into Nifti format and stored in the NAS (Network-Attached Storage).
  6. Select and Apply Study Card : the user has to choose a Study Card which matches the examination Centre and the import-related Clinical Study.

Import Source

It is possible to import data from several different sources

From a DICOM CD/DVD

Data Import from a DICOM CD/DVD is available. However, due to systems constraints, it is not possible to import data directly from your CD/DVD drive.

You need first to create an achive zip from the DICOM CD/DVD. To do so, just use your favourite archiver and compress the DICOM CD/DVD from the root.

Exemple sous Windows

You just need to right click on the CD/DVD. Then, choose something like “Compress Folder” / “Archive Folder” depending on your archiver. Mind to choose the zip format.

compression CD/DVD Dicom

Once the zip archive is ready, you must upload it into Shanoir server. To do so, just click on Add… button and select the previously created zip file:

upload dicom zip

Warning: the archive you are trying to upload is checked and must contain a DICOMDIR file at the root.

From DICOM associations

From Files

Preferences Menu

Général

Modifier son profil

Administration

Gérer les utilisateurs

Gérer les droits sur les études

Modifier les valeurs des entités de référence

Les utilisateurs possédant le profil “Administrateur” sont autorisés à modifier les valeurs de certaines entités de référence. Dans la base de données, cela correspond aux tables dont le nom commence par “REF_*”. Pour atteindre cette fonction, il faut se rendre dans le menu “Administration > Modification des constantes”.

Study Card

Une Study Card est un moyen utilisé pour l'import de données qui a pour objectif de faciliter l'import pour les utilisateurs.

Une Study Card peut être vue comme une carte de protocole qui inclut des paramètres qui permettront d'assigner automatiquement certaines valeurs à certains champs de la base de données. En effet, pour un utilisateur non averti, il est difficile de savoir comment renseigner des champs dont la sémantique est liée à l'ontologie sur laquelle se base Shanoir.

Une Study Card est définie pour un couple (centre, étude). Il peut y avoir plusieurs Study Cards pour un même couple (centre, étude).

Qui définit les Study Cards ?

Les Study Cards peuvent être créées/supprimées/modifiées uniquement par des utilisateurs dont le profil est Expert, Medical ou Administrator. La création/suppression/modification des Study Cards peut être faite dans l'onglet Administration>Manage Study Cards. La création de Study Card peut également se faire lors du processus d'import de données.

Comment créer une Study Card ?

Pour créer une Study Card il faut tout d'abord lui donner un nom unique. Il faut ensuite choisir l'étude et le centre pour lesquels la Study Card est créée. Il faut ensuite ajouter les paramètres de configuration. Pour cela, il est possible de définir 2 types de configuration :

  1. Paramètres systématiques
  2. Paramètres conditionnels en fonction de Tags Dicom

Paramètres systématiques

Ce sont des paramètres qui seront appliqués systématiquement Par exemple :

Paramètres systématiques

La première colonne correspond à la table de la base de données. La seconde colonne correspond à la colonne de la table sélectionnée La troisième colonne (suivant le cas le cas, ce peut être un champ texte) correspond à la valeur assignée à la colonne de la table. La case à cocher indique si l'utilisateur qui sélectionne cette Study Card est autorisé à modifier la valeur du champ systématique.

Paramètres conditionnels en fonction de Tags Dicom

Il est également possible de définir des parmètres en fonction des Tags Dicom des séries à importer. Il est ainsi possible de définir pour n'importe quel tag Dicom l'algorithme suivant :

si Tag.DICOM == 'value' alors
   // appliquer paramètre systématique
fsi

Voici un exemple :

Paramètres systématiques

La première colonne de la première ligne correspond au Tag Dicom. La seconde colonne de la première ligne correspond à la valeur conditionnelle du Tag Dicom. La seconde ligne est identique aux paramètres systématiques décrits précédemment.

Comment utiliser les Study Cards ?

Au moment de l'import, il suffit de sélectionner la Study Card adéquate lorsque le choix de la Study Card s'offre à l'utilisateur.

Nifti Converters

Since Shanoir 1.0.0, there is the possibility of using different Nifti converters in multiple versions. By multiple, I mean two : dcm2nii and mcverter as they are the most used and the most reliable. But each version comes up with differents results, depending of the MRI device used for example.

To see which nifti converters are already available, go to : Administration → Manage Nifti Converters

Then is the list presenting all existing converters. A converter is defined by its name, type (dcm2nii, mcverter or clidcm (old Shanoir versions)), version and if it's active or not.

There is no way to delete an existing converter because there should always be at least one available converter. The only way is to deactivate the converter through converter edition. To edit a converter, click on the edit icon, in the corresponding line in the list.

Creating / Editing a nifti converter

Here is the creation/edition page of a nifti converter :

To define a converter, first select a converter type (dcm2nii or mcverter). Then enter the exact name to the converter executable. Mcverter and dcm2nii do not require installation. Executable file will work alone, so there can be multiple versions of a same converter type on a same server. All executables files will be stored in a same folder containing all executables of all versions and set in the Shanoir.properies file under : path.to.nifti.converters.linux or path.to.nifti.converters.windows

For example, to add a dcm2nii version, rename the dcm2nii to the corresponding version you want to set up : dcm2nii_2008-03-31 And put it in the folder for example : /usr/bin/nifti-converters/dcm2nii_2008-03-31

So to use this version of the dcm2nii converter, just set the converter name to dcm2nii_2008-03-31.

Make sure type and converter executable are the same or you will get an incompatibility error. Same thing if the executable does not really exists.

To activate or deactivate a converter, just modify the is_active flag to Yes or No.

Finally, a free comment is available.

If everything has been correctly set, the converter is created/updated and available.

Converter in study cards

To keep datas homogeneity, a converter is linked to a study card. So for a same center/machine, nifti files are converted with the same converter.

To choose a converter for a study card, just go to the edit study card page and select on of the active converters.

When importing, DICOM files will be converted to nifti using this converter corresponding to the chosen importing study card.

Regenerate Nifti files

Sometimes, the nifti conversion may have failed during import, or a user wants to use a dataset with a different converter. It is now possible to convert existing dataset DICOM files without another import. Go to viewDetailDataset page. Under the “Available Nifti files to download for this dataset” is the list of already converted nifti files. (At least the nifti files generated during import). It gives the converter and its version used to obtain those files.

To regenerate files, click on the ”(Re)Generate Nifti Files for this dataset” and select another study card/converter couple. Then click Generate. If corresponding nifti files do not already exist, the conversion begin. When the conversion is done, there is a new link under the Available Nifti files.

You can now download those newly converted files.

Download Nifti files

Among the viewDetailDataset page, Nifti files can be downloaded directly in the dataset list page (manageDatasetOpt). Just click on the folder and arrow icon and select Download nifti files. You can choose which version of the nifti files you want to download (if multiple versions exist). At least there will always be the version created during import and corresponding to the version attached to the study card.

Multiple dataset nifti download is available the same way.

Limitations

Conversion Nifti : .bvec et .bval

Expliquer le souci de nommage avec les données DTI + expliquer le possible écrasement si ajout de données pour le même patient et même examen.


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