Difference between revisions of "Documentation/4.0/SlicerApplication/LoadingData"

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__NOTOC__
 
=Introduction=
 
=Introduction=
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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.  
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Slicer can load a large variety of data in multiple ways. For Dicom data, please refer to the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module documentation. For almost everything else (including scenes), you can use the '''Add Data''' dialogue. For a listing of supported data formats see [[Documentation/{{documentation/version}}/SlicerApplication/SupportedDataFormat|here]]. Please note that some of the formats listed are only partially supported.
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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.<br>
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Images can be read into Slicer using the '''Add Volume''' dialog. The '''Add Data''' dialog can be used to load most of all other types of data formats that Slicer can handle, including <code>.tiff</code>, <code>.jpeg</code>, <code>.nrrd</code>, <code>.vtk</code> 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 <code>nrrd</code> file using the '''DICOM to nrrd converter''' and then to load the nrrd file into Slicer.
+
For some of the more complicated formats (DWI in particular) it is recommended to first convert the DICOM data into the <code>nrrd</code> format using the [[Documentation/{{documentation/version}}/Modules/DicomToNrrdConverter|DICOM to nrrd converter]] and then to load the nrrd file into Slicer. Many vendors are using non standard ways to describe their DWI data in the DICOM headers. The DICOM to nrrd documentation contains a listing of specific formats that have been debugged and tested.
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{{warning}} See http://www.slicer.org/slicerWiki/index.php/Modules:Loading-Data-3.6
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{|align="center" border="1" style="text-align:center; font-size:120%; border-spacing: 0; padding: 0px;" cellpadding="10"
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|[[#Add Data| Add Data ]]
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|[[#Add DICOM Data| Add DICOM Data ]]
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|[[#Misc.| Misc. ]]
 +
|}
  
 
=Add Data=
 
=Add Data=
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The '''Add data''' dialog allows you to select individual datasets to add to the existing scene.
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The '''Add Data''' dialogue allows you to load virtually any type of data that Slicer can handle. It should be used as the default way of loading data, with the exception of DICOM, which has its own interface. Data is added to the existing scene.
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[[Image:SlicerApplication-AddData-Empty.png|center|Add Data]]
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<gallery widths="300px"  heights="200px" perrow="4">
 +
image:SlicerApplication-AddData-Empty.png|[[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts|CTRL-A]] is an application-wide key combination for bringing up the Add Data dialogue.
 +
image:SlicerApplication-FileAddData.png|File/Add Data contains another link to bring up this dialogue
 +
image:SlicerApplication-AddData-SlicerWelcome-mj.png|Shortcuts to the dialogue are in the Load/Save toolbar and in the [[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome]] module
 +
</gallery>
  
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===There are 3 ways to open the dialog===
 
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*From the '''File''' menu
 
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[[Image:SlicerApplication-FileAddData.png|File/Add Data]]
 
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*From the [[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome]] module
 
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[[Image:SlicerApplication-AddData-SlicerWelcome.png|Add Data from Welcome module]]
 
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*Using the application wide shortcut [[Documentation/{{documentation/version}}/SlicerApplication/KeyboardShortcuts|CTRL-A]]
 
  
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===The dialog exposes the following functionality===
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==="Add Data" Functionality===
 
*The '''Choose Directory to Add''' button adds all files inside the selected directory to the file list.
 
*The '''Choose Directory to Add''' button adds all files inside the selected directory to the file list.
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*The '''Choose Files(s) to Add''' button adds all selected files to the file list.
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*The '''[[#"Choose" File Dialogue|Choose Files(s) to Add]]''' button adds all selected files to the file list.
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*The '''Show Options''' checkbox shows/hides the option column to control loading properties.
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*The '''[[#Show Options|Show Options]]''' checkbox shows/hides the option column which controls properties assigned to an object at loading time. Here you can identify a file as a label map or a streamline.
 
*The '''Reset''' button clears the entire list of files to load.
 
*The '''Reset''' button clears the entire list of files to load.
 
*The '''Ok''' button loads all datasets in the list, and
 
*The '''Ok''' button loads all datasets in the list, and
 
*The '''Cancel''' button aborts the entire load.
 
*The '''Cancel''' button aborts the entire load.
  
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===Choose File(s)===
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==="Choose" File Dialogue===
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After clicking on the “Choose Files to Add” button, a file dialog opens.
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<gallery widths="300px" heights="200px">
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[[Image:SlicerApplication-AddData-ChooseFiles.png|center|Choose File(s) to Add]]
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image:SlicerApplication-AddData-ChooseFiles.png|After clicking on the “Choose Files to Add” button, a new File Dialogue opens. <br> It is possible to select multiple files using '''CTRL-click''' and multiple contiguous files with '''SHIFT-click'''.
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It is possible to select multiple files using ''CTRL-click'' and multiple contiguous files with ''SHIFT-click''.<br>
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image:SlicerApplication-AddData-ChooseFiles.png|Selecting a <code>.mrml</code> file will '''add''' the scene. When loaded, it will load all the objects contained in that scene. It is not necessary to individually select those files.
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{{warning}} Selecting a <code>.mrml</code> file will load all the files referenced in the scene; it is not necessary to manually select those files, they would be loaded twice.
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</Gallery>
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===Review files before loading===
 
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Once the files are selected in the '''Choose File(s)''' dialog, they are listed in the '''Add Data''' dialog.
 
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[[Image:SlicerApplication-AddData-SelectedFiles.png|center|Add Data after selection]]
 
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You can review the selected files, and ensure they will be correctly loaded.
 
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*The checkbox in the '''File''' column control whether to load the file or not.
 
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*The '''Description''' column shows the type of file automatically detected.
 
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It is used to select the reader to load a file. Some file extensions (e.g. <code>.vtk</code>) can contain different types, e.g. ''Volumes'', ''Models'' or ''Fiber bundles''. You must ensure the correct type is selected.
 
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[[Image:SlicerApplication-AddData-ChangeType.png|center|Change file type]]
 
−
Some types (e.g. ''Volumes'' or ''Scalar Overlay'') can take extra parameters before loading
 
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*Checking the box of '''Show Options''' shows a new column that contains the loading options if any.
 
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[[Image:SlicerApplication-AddData-ShowOptions.png|center|Change file type]]
 
−
 
 
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=Add Volume Data=
 
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The '''Add Volume''' dialog allows you to load volume files into the existing scene.
 
−
[[Image:SlicerApplication-AddVolume.png|center|Add Volume]]
 
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===There are 2 ways to open the dialog===
 
−
* From the '''File''' menu
 
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[[Image:SlicerApplication-FileAddVolume.png|File/Add Volume]]
 
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* From the [[Documentation/{{documentation/version}}/Modules/SlicerWelcome|Welcome]] module
 
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[[Image:SlicerApplication-AddVolume-SlicerWelcome.png|Add Volume from Welcome module]]
 
  
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===At the bottom of the dialog, a list of components controls the loading of the selected volume(s)===
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===Show Options===
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*'''Node name''' input box: the name (by default: filename with no extension) that refers to the volume within Slicer
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<gallery widths="350px"  heights="200px">
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*'''Centered''': ignore the position information from the file and center the volume on (0,0,0) instead
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image:SlicerApplication-AddData-SelectedFiles.png|Once the files are selected in the '''Choose File(s)''' dialogue, they are listed in the '''Add Data''' dialogue.
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*'''Ignore orientation''': ignore the orientation information from the file and use the Identity instead
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image:SlicerApplication-AddData-ChangeType.png|You can review the selected files, and ensure that they were properly identified before loading.<br> The checkbox in the '''File''' column controls whether to load the file or not. This is handy, if you change your mind about which files to load.<br> The '''Description''' column shows the type of file automatically detected.
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*'''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.
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It is used to select the reader which loads a file. Some file extensions (e.g. <code>.vtk</code>) can contain different types, e.g. ''Volumes'', ''Models'' or ''Fiber bundles''. You must ensure the correct type is selected.
−
*'''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.
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image:SlicerApplication-AddData-ShowOptions.png|Some objects (e.g. ''Volumes'' or ''Scalar Overlay'') can take additional specifications before loading<br>Checking the '''Show Options''' box results in the display of additional columns containing loading options, if any.
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[[Image:SlicerApplication-AddVolume-SingleFile.png|center|Uncheck Single File when volume is within multiple files]]
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</Gallery>
  
 
=Add DICOM Data=
 
=Add DICOM Data=
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Please refer to the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module documentation.
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Beginning with Slicer 4.0, Slicer holds DICOM data in a local data base. DICOM data can be imported from disk or retrieved from a PACS system (after proper setup).
 +
* For more information about this module, please refer to the [[Documentation/{{documentation/version}}/Modules/DICOM|'''DICOM''']] module documentation.
 +
<gallery widths="550px"  heights="200px">
 +
Image:DicomModule-2012-02-21.png|The Dicom Module uses a pop-up to provide information about the selected data set.
 +
Image:LoadSaveToolbar-mj.png| Shortcuts to the dialogue are in the Load/Save toolbar and in the Welcome module
 +
</Gallery>
  
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=Add Sample Data=
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=Misc.=
−
Please refer to the [[Documentation/{{documentation/version}}/Modules/SampleData|Sample Data]] module documentation.
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==Add Sample Data==
 +
This module downloads a number of sample data sets from the internet. These data sets can be used for testing of slicer capabilities.
 +
* For more information about this module, please refer to the [[Documentation/{{documentation/version}}/Modules/SampleData|'''Sample Data Module''']] documentation.
 +
<gallery widths="350px"  heights="200px">
 +
Image:SampleData2012-02-21.png|The Sample Data Module allows downloading of sample data from a webserver.
 +
</Gallery>
  
−
=Favorites=
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==Favorites==
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[[Image:SlicerApplication-Favorites.png|center|Favorites in file dialog]]
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In order to quickly navigate to particular locations in your file system, it is possible to define shortcuts, also known as '''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.
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<gallery widths="350px"  heights="200px">
−
[[Image:SlicerApplication-Favorites-Add.png|center|Drag and drop to add a new Favorite]]
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Image:SlicerApplication-Favorites.png|Favorites are visible in the left column of the "File Dialogue"
−
To create a symbolic link, you drag&amp;drop a directory from the right panel to the left panel. It will be remembered next time you start slicer.
+
Image:SlicerApplication-Favorites-Add.png|Drag and drop from the list of folders on the right in order to create a new Favorite
 +
</Gallery>
  
 
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Latest revision as of 07:34, 14 June 2013

Home < Documentation < 4.0 < SlicerApplication < LoadingData


For the latest Slicer documentation, visit the read-the-docs.



Introduction

Slicer can load a large variety of data in multiple ways. For Dicom data, please refer to the DICOM module documentation. For almost everything else (including scenes), you can use the Add Data dialogue. For a listing of supported data formats see here. Please note that some of the formats listed are only partially supported.

For some of the more complicated formats (DWI in particular) it is recommended to first convert the DICOM data into the nrrd format using the DICOM to nrrd converter and then to load the nrrd file into Slicer. Many vendors are using non standard ways to describe their DWI data in the DICOM headers. The DICOM to nrrd documentation contains a listing of specific formats that have been debugged and tested.

Add Data Add DICOM Data Misc.

Add Data

The Add Data dialogue allows you to load virtually any type of data that Slicer can handle. It should be used as the default way of loading data, with the exception of DICOM, which has its own interface. Data is added to the existing scene.

  • CTRL-A is an application-wide key combination for bringing up the Add Data dialogue.

  • File/Add Data contains another link to bring up this dialogue

  • Shortcuts to the dialogue are in the Load/Save toolbar and in the Welcome module


"Add Data" 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 which controls properties assigned to an object at loading time. Here you can identify a file as a label map or a streamline.
  • 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 Dialogue

  • After clicking on the “Choose Files to Add” button, a new File Dialogue opens.
    It is possible to select multiple files using CTRL-click and multiple contiguous files with SHIFT-click.

  • Selecting a .mrml file will add the scene. When loaded, it will load all the objects contained in that scene. It is not necessary to individually select those files.

Show Options

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

  • You can review the selected files, and ensure that they were properly identified before loading.
    The checkbox in the File column controls whether to load the file or not. This is handy, if you change your mind about which files to load.
    The Description column shows the type of file automatically detected.

  • Some objects (e.g. Volumes or Scalar Overlay) can take additional specifications before loading
    Checking the Show Options box results in the display of additional columns containing loading options, if any.

Add DICOM Data

Beginning with Slicer 4.0, Slicer holds DICOM data in a local data base. DICOM data can be imported from disk or retrieved from a PACS system (after proper setup).

  • For more information about this module, please refer to the DICOM module documentation.

  • The Dicom Module uses a pop-up to provide information about the selected data set.

  • Shortcuts to the dialogue are in the Load/Save toolbar and in the Welcome module

Misc.

Add Sample Data

This module downloads a number of sample data sets from the internet. These data sets can be used for testing of slicer capabilities.

  • For more information about this module, please refer to the Sample Data Module documentation.

  • The Sample Data Module allows downloading of sample data from a webserver.

Favorites

In order to quickly navigate to particular locations in your file system, it is possible to define shortcuts, also known as Favorites.

  • Favorites are visible in the left column of the "File Dialogue"

  • Drag and drop from the list of folders on the right in order to create a new Favorite

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