Browser Area
What is it for?
The browser area allows you to import data into a database, which you can populate from external files or sources.
Source Selector
The Source Selector offers a choice of tabs listing the data available in different sources:
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Database: the database of data imported into medInria. This may include temporary data generated by some algorithm, or temporary imported just for the duration of one session of medInria.
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File System: this lists the data available on the local filesystem for import.
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PACS/CD: allows you to read Dicom Dirs on the local file system (like cds), or to interrogate a PACS.
The File System tab
Browse your file system
Browse the file tree of your computer to display the data you want to import:
- Directly in the browsing area.
- Or, with the current tree location above the browsing area.
- Or, with the file tree just under the "File system" tab.
You can bookmark directories right-clicking on them in the Browsing area, and chose "Bookmark". They are displayed in the panel under the "File system" tab.
Import data
Select one or more data that you want to import. If you want to import a DICOM, you need to select the DICOM directory.
Then choose an import button or right-click on the data:
- View: the selected data is temporary imported, then displayed into the Visualization workspace.
- Temporary Import: the selected data is loaded into a temporary database. If the application is closed without saving it, it will be lost. Temporary data is shown in italics in the database.
- Import: the selected data are copied into your application local database. The data will be available the next time you open the application, even if the original file has been removed.
In the Database tab, or in any imagery workspace database column, you can permanently save a temporary data right-clicking on the data and choosing "Save".
Supported formats
medInria can import/export:
- ITK supported file format: DICOM, VTK, mha, NIFTI, GDCM, GIPL, Nrrd, GIS, etc.
- VTK meshes with metadata from field data.
- Scenes: xml describing a view and export of each layer of this view.
- JPEG, BMP (2D), TIFF (2D).
The Database tab
Once imported, data is shown in the Database tab, which is a tree structure organised by a Patient/Study/Series hierarchy, following the DICOM precepts. In italics are the temporary data.
Interactions with the tab are:
- Double clicking on a data row switches to the Visualization workspace with the data opened in the view.
- Right clicking on a row allows you to perform actions according to the type of row (patient/study/series) for instance for a series edit, view, export or remove a data, or read its metadata.
If a row is a Study, the action will be applied to all the series below it, and if it is a Patient, to all its studies, and as result series.
Filters can be used to reduce the size of the displayed data. Filters are added by selecting a field name. Only one field of each type is possible, you can delete a filter by selecting its name in the drop down list of fields and clicking on the minus sign.
The PACS/CD tab
This part is under (re)construction, it's too old.
DICOM data source
The DICOM datasource looks at a DICOM dir as if it was a small database, and allows queries on remote PACS systems. The top row gives you search criteria: Patient name, Study descritption, Series description, modality, gender, and filters between two dates.
Patients, studies and series will be displayed in 3 different lists, Studies and Series being updated given the selected patient and study.
SCU configuration
medInria acts as a SCU: Service Class User in the DICOM terminology. Prior to any DICOM query to a SCP (Service Class Provider) the application needs to identify itself as a SCU. This is done in the top right tool box. The user must specify :
- AE Title, that will identify the SCU on the network
- The TCP incoming port. The port that will be used by the SCP to send data.
- The hostname, that will allow the SCP to locate the machine. As any TCP-IP hostname it can be an IP address or a name known to a DNS server.
Server configuration
The tool box below, called DICOM servers settings, holds a list of registered known SCPs. Before saving an entity, the user must fill in server hostname, AE Title, TCP port and the name it will be listed by in the top left list of servers.
There is an echo button in order to test a value before saving it. It sends the DICOM echo message to DICOM servers.
Importing from DICOM services to the local DB
The next two tool boxes underneath will give some information useful before importing any data. The last tool box brought by the dicom plugin is the import in database one. It imports the selected series into the database. Notice that it is not possible to index or load the data, only import it at the moment.
Importing composite DTI data ?
WARNING: Currently composite data sets is just a technological preview. The datasets can be imported and saved in the database but cannot be used directly from any other medInria plugin from the time being. It is intended to add functionality to the next medInria release to create and use these composite datasets from some plugins.
A composite data set is a way to associate multiple data together. Take for example, a raw DTI data set. Such a dataset contains several images and each of these images is associated to a gradient direction (which is not always available in the image meta-data). As a user, it would be nice to manipulate all these images and their associated gradient as a whole. This is true for the visualization plugins, the processing plugins and also for the database (you usually do not want to have one entry for each of the tens of images which constitute the dataset).
Technically, a composite dataset is simply a zip container that gathers all the needed data in a single file. Typically, the zip will be expanded to a directory containing the individual files and a simple text file that will list them and associated the needed metadata.
Here is for example, the structure of a composite dataset made for DTI images:
unzip -l dwi.cds
Length Date Time Name
--------- ---------- ----- ----
0 08-14-2011 02:01 dwi/
1900842 06-21-2011 14:36 dwi/wholedataset-0.mha
1900842 06-21-2011 14:36 dwi/wholedataset-6.mha
1900842 06-21-2011 14:36 dwi/wholedataset-5.mha
1900842 06-21-2011 14:36 dwi/wholedataset-2.mha
1900842 06-21-2011 14:36 dwi/wholedataset-3.mha
1900842 06-21-2011 14:36 dwi/wholedataset-4.mha
272 08-14-2011 02:01 dwi/Description.txt
1900842 06-21-2011 14:36 dwi/wholedataset-1.mha
--------- -------
13306166 9 files
This simple example shows two things, the dwi.cds is a simple zip file. Consequently, you can continue to manipulate the data it contains with other tools (just unzip it, change the files and rezip it). Second, the file dwi.cds is simply expanded into a directory dwi that contains the various images plus a metadata text file named dwi/Description.txt. Here is the content of this file:
# MEDINRIA COMPOSITE DATA: DWI 1.0
# A DTI dataset
Images: 7 MetaData: 0
"wholedataset-0.mha" [0 0 0]
"wholedataset-1.mha" [1 0 1]
"wholedataset-2.mha" [-1 0 1]
"wholedataset-3.mha" [0 1 1]
"wholedataset-4.mha" [0 1 -1]
"wholedataset-5.mha" [1 1 0]
"wholedataset-6.mha" [-1 1 0]
In this example, we see that the Description.txt file is a simple text file. Blank lines are ignored, Comments start with the '#' character and run till the end of the line. The first line is special and acts as a magic cookie to identify a composite dataset (the "# MEDINRIA COMPOSITE DATA:") followed by the type of composite data (here "DWI" for diffusion weighted images) and a version (currently unused). Everything else is specific to the DWI file format, here it is just stated that there are 7 images and special metadata section (metadata are directly associated to the images). Then, there is a list of image names (contained in the dwi directory) and their associated gradients.
The whole dwi.cds containing this information can be imported as a whole in the database (currently this is the only operation permitted) as any other file. See section "How to import".