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MRQuantif - Configuration and choice of preferences

This tab is used to configure the default values ​​used in the software and options or operating parameters such as exchanges with internet (update and export of data), communication with PACS (import and export) ...


It is possible to interface the software with a PACS. The principle is simple:

  • PACS must allow the export of a selection of either an examination or one or more series or all the echoes of the same sectional plane of a series
  • the PACS must export these compressed or uncompressed DICOM images into a disk directory (preferably the fromPACS directory at the root of the MRQuantif main directory) or via a DICOM store to the SCP defined in the options below
  • and if possible the PACS must launch, at the end of the export, the software MRQuantif (otherwise it will have to be launched independently).
  • The software MRQuantif will scan the directory fromPACS to list the images present. You can define by the field Import from PACS another directory to be scanned by default. As a precaution, this directory must be empty to be selectable as an import directory because its contents are deleted at each closure.
  • MRQuantif, after analysis, can re-export if an export mode is chosen via the drop-down menu Export mode a copy of the viewer showing the selected ROIs and their position. It can also export a copy of the curves of each series analyzed. Up to know the report is not exported to the PACS.
  • MRQuantif deletes all files from the fromPACSdirectory, or only all DICOM files if it is closed. This is another default directory.

The field used to specify the main directory of the PACS software is used in the automatic integration with PACS Telemis, the only choice currently possible and therefore not modifiable. Other automated integrations will definitely be possible in the future.

If the path to the PACS software is empty, the presence of the PACS Telemis software is searched for at launch and if it is found the path falls within this field. It is also possible to manually specify the directory position telemis_tmrhe or its equivalent. The installation allows you to create a plugin configuration file MRQuantif.plugin.telemis.cfg in the directory ... \ telemis_tmrhe \ telemis \ entity \ tmrhe \ cfg \ imageProcessingPlugins and place the software icon in the directory ... \ telemis_tmrhe \ telemis \ entity \ tmrhe \ cfg \ icon. Thus at the launch of the Telemis software the configuration is defined and the plugin can be selected to be integrated into the toolbar.

The export configuration is defined by Export mode :

Export to PACS can be done:

  • either in the export directory defined in the field Export to PACS
  • or by DICOM communication (DICOM store SCU defined below):
    • manual showing, when all the ROIs have been placed, a small window containing a send button:
    • or automatic at the end of the analysis of an examination with return to the browser or when closing the software

The content of the export is defined by the selection Export content.

DICOM store provider (SCP) function

A DICOM "receiver" is attached to the software. It can be used or not, independently or not. The reception parameters are definable in this part:

If the receiver is "on" MRQuantif launches, when it opens, the windows command file (but this could also be another executable) [ 53] mrq_scp.bat present in the directory MRQuantif. We then obtain a windows command window in which we will scroll in real time the arrival of DICOM files. You do not have to close this window but you can hide it.

If you want the receiver to be launched as soon as you open the session or even the computer, you have to set up an automatic launch via the registry and thus have the rights and the skills to make this configuration.

This batch file looks for the java8 and launches the command java which can be modified and launched independently,

  • with the java8 installed:
     java -cp ./MRQuantif.jar com.pixelmed.network.StorageSOPClassSCPDispatcher "104" "mrquantif" "./fromPACS" 0
  • with the adjacent jer in the MRQuantive :
    directory. bin \ java.exe -cp ./MRQuantif.jar com.pixelmed.network.StorageSOPClassSCPDispatcher "104" "mrquantif" "./fromPACS" 0

We find, in this command line, the parameters corresponding to the port "104 ", the AET" mrquantif ", the reception directory" ./fromPACS "and a last numeric parameter 0 that must not be changed.For more information on this function see the Pixelmed documentation.

DICOM store user (SCU) function

A DICOM "sender" is attached to the software. The parameters of this function can only be entered if the export via "DICOM store" has been selected in Export mode. The parameters of the DICOM SCP of the PACS must be entered:

Processing and fitting

The default values ​​of the various parameters used during the processing and in particular the T2 * / R2 * can be defined. These are the default values ​​that will be used for iterative uses of the software and not the values ​​of the current analysis. These will not be changed except for the options present only here (essentially the number of fat peaks and the noise level determination mode):

The available options are detailed in section Results.


Here you can set the default language for writing reports. As before, this is also the default value that will be used in iterative uses of the software and not in the language of the current report.

Import and select

Here we can define the behavior of the DICOM file browser:

  • autoimport : allows to scan automatically or not the import directory defined above
  • autobrowse : allows to scan automatically or not manually selected directory
  • autoimport : allows to select automatically or not images and open the viewer if there are only images of the same section plane.

As before, for autobrowse and autoselect it is here again also the default value which will initialize the checkboxes present on the page Browser.



You can configure the use of the Internet connection if it exists: [ 88] check update : allows search automatically if a new version is available. If this is the case a modal window will tell you the new features of the proposed version and allow you to load it. This loading is done in the background and will not bother you. When you leave the software the update will be done so that the new version is available at the next launch.

  • show beta versions : allows to extend the search for the new versions by also accepting the versions in the phase of test.
  • save data (de-identified) : if this option is checked, an anonymized data export will occur to the central server and you will be able to find the trace of this data but without a name and with a date of


Local saving in my_data folder

This area allows you to configure the content saved locally in the directory my_data :

  • Selected DICOM images : by default the images selected for the analysis are kept. This option is not currently de-selectable.
  • JSON file for database : The JSON format is a format similar to XML. It is readable via on-line tools.This option is not currently de-selectable.
  • de-identify local data : if this option is checked the name of the directory of the Patient will be anonymized as well as DICOM images, JSON file, and screenshots saved in this directory. This allows you to meet the standards of the CNIL on a self-service PC. However, if the directory my_data is on a disk accessible by a session protected by CNIL standards, you can keep the identification and make an appropriate declaration.
  • CSV file for Excel : if this option is checked it will be created at the top level of the directory my_data a CSV file (compatible Excel) which will contain one line per series. Warning this file is not currently anonymous and you must secure its access. This option is not useful in routine.
  • Curve graph in JPEG : this option is checked by default and is not currently modifiable. It makes it possible to store a screenshot (anonymous or not, see above) of the curves locally.
  • Report in RTF : this option is not yet activated.

Advanced functions

Three functions In this area, you can define:

  • Protocols : By default, the selection of a search protocol is hidden "Hide". If enabled, a pop-up menu will appear in the top banner to select the protocol. The configuration of the protocols is not accessible simply to the user but is done via the configuration file. This can only be used for particular configurations within a search protocol.
  • Import : this gives the possibility of importing a csv file to recalculate results from measurements already made.eci can only be used for particular configurations that are part of a search protocol
  • Logs : this function is not perfectly finalized and can only be used in development mode or with an output in the command file (the software must be launched via the batch file.)


Via the drop-down menu, you can select a user to modify his data or add a user.

there are several defined users one can select a default user or leave the choice to force the selection on opening by choosing "Select ..."


Only one institution can be described.