Documentation/4.0/SlicerApplication/LoadingData

Introduction

Slicer can load a large variety of data in multiple ways. From the general Add Data dialog to the more module-specific dialogs, many file formats are supported. The data module allows to load scenes and individual datasets of many types, and to view the scene's data hierarchy. Here we will describe the all purpose file dialogs.
The Add Data dialog can be used to load most of all other types of data formats that Slicer can handle, including .tiff, .jpeg, .nrrd, .vtk and many other formats. For some of the more complicated formats (DWI in particular) it is recommended to first convert the DICOM data into the nrrd file using the DICOM to nrrd converter and then to load the nrrd file into Slicer. Images can be read into Slicer using the Add Volume dialog.

Add Data

The Add data dialog allows you to select individual datasets to add to the existing scene.

There are 3 ways to open the dialog

• From the File menu

• From the Welcome module

• Using the application wide shortcut CTRL-A

The dialog exposes the following functionality

• The Choose Directory to Add button adds all files inside the selected directory to the file list.
• The Choose Files(s) to Add button adds all selected files to the file list.
• The Show Options checkbox shows/hides the option column to control loading properties.
• The Reset button clears the entire list of files to load.
• The Ok button loads all datasets in the list, and
• The Cancel button aborts the entire load.

Choose File(s)

After clicking on the “Choose Files to Add” button, a file dialog opens.

It is possible to select multiple files using CTRL-click and multiple contiguous files with SHIFT-click.
Warning: Selecting a .mrml file will load all the files referenced in the scene; it is not necessary to manually select those files, they would be loaded twice.

Review files before loading

Once the files are selected in the Choose File(s) dialog, they are listed in the Add Data dialog.

You can review the selected files, and ensure they will be correctly loaded.

• The checkbox in the File column control whether to load the file or not.
• The Description column shows the type of file automatically detected.

It is used to select the reader to load a file. Some file extensions (e.g. .vtk) can contain different types, e.g. Volumes, Models or Fiber bundles. You must ensure the correct type is selected.

Some types (e.g. Volumes or Scalar Overlay) can take extra parameters before loading

• Checking the box of Show Options shows a new column that contains the loading options if any.

Add Volume Data

The Add Volume dialog allows you to load volume files into the existing scene.

There are 2 ways to open the dialog

• From the File menu

• From the Welcome module

At the bottom of the dialog, a list of components controls the loading of the selected volume(s)

• Node name input box: the name (by default: filename with no extension) that refers to the volume within Slicer
• Centered: ignore the position information from the file and center the volume on (0,0,0) instead
• Ignore orientation: ignore the orientation information from the file and use the Identity instead
• LabelMap: flag the volume as a labelmap, it will behave differently by default (no linear interpolation, use a lut…). By default, files containing the word “seg” are automatically flagged as LabelMap.
• Single File: control whether the volume is defined within one or multiple files. For example a stack of 2D image files to make a 3D volume. This is usually the case with DICOM files. When a volume is made of multiple files, select only the first file and uncheck the Single File checkbox.

Add DICOM Data

Please refer to the DICOM module documentation.

Add Sample Data

Please refer to the Sample Data module documentation.

Favorites

When searching for files, in order to quickly find your data, it is possible to use favorites, symbolic links saved and restored for each session.

To create a symbolic link, you drag&drop a directory from the right panel to the left panel. It will be remembered next time you start slicer.