DICOMBrowser-3.6 - Revision history

Wjp at 13:57, 10 June 2010

2010-06-10T13:57:35Z

Wjp: /* Non-DICOM Files */

2010-06-10T13:56:12Z

Non-DICOM Files

Wjp: /* Volumes */

2010-06-10T13:55:35Z

Volumes

Wjp: /* Volumes */

2010-06-10T13:54:20Z

Volumes

Wjp: /* Volumes */

2010-06-10T13:50:36Z

Volumes

Wjp at 13:35, 10 June 2010

2010-06-10T13:35:03Z

Wjp: Created page with 'Return to Slicer 3.6 Documentation Return to Loading Tractography Data Documentation NOTOC == General Information == ===…'

2010-06-10T13:34:01Z

Created page with 'Return to Slicer 3.6 Documentation Return to Loading Tractography Data Documentation __NOTOC__ == General Information == ===…'

New page

[[Documentation-3.6|Return to Slicer 3.6 Documentation]]
[[Loading Tractography-3.6|Return to Loading Tractography Data Documentation]]

__NOTOC__
== General Information ==

=== Scenes ===

Loading existing slicer scene files (for example, mrml files created using the [[Modules:Saving-Documentation-3.4| File->Save dialog]] is pretty easy. Just use File->Load Scene... and browse to the .mrml file to load it. This replaces your existing scene.

You can also use File->Import Scene... to ''add'' the contents of a scene file into your existing scene.

=== Volumes ===

[[Image:AddVolume.png|thumb|300px|right|The Add Volume dialog]]

The File->Add Volume... dialog is specialized for loading volume data files, and has special features to help load DICOM files.

==== Non-DICOM Files ====

This is primarily a file browser, so for most volume types (.nrrd, .nii, etc) you can just browse to the file you want and click Apply.

The Path field can be used to quickly get to a directory or file, for example if you want to paste in a directory path from another window.

Slicer 3.4 can read the file types supported by [http://www.itk.org ITK version 3.10].

==== DICOM Files ====

If you browse to a DICOM file, the contents of the file header will be shown in the lower portion of the DICOM Information box.

When you have browsed to a directory that contains DICOM files, you can click the Parse Directory button to generate a tree that is organized as follows:

* '''Patient'''
* '''Study'''
* '''Series'''
* '''Files'''

Slicer assembles the files within a '''Series''' as a Volume for display and analysis purposes. Since certain scanners may put multiple volumes in the same series, slicer also breaks some collections of files based on certain content fields. In the example shown in the figure, series "TSE65_trig" has 32 files that were acquired as 4 sets of 8 images for 4 distinct trigger times. By selecting different nodes in the tree, the user can pick which set of files to load as a volume.

The DICOM tree information is stored in a cache so that it can be displayed more quickly on subsequent views. You may need to re-parse the directory if you have added new DICOM files to the directory.

==== Volume Options ====

* '''Centered''' ignores any Origin or ImagePositionPatient tags in the volume data and instead centers the volume around 0,0,0.
* '''Ignore File Orientation''' ignores any Direction Cosines, Space Directions, or ImageOrientationPatient tags in the volume data.
* '''Label Map''' reads the volume as a label map that can be used, for example, with the Model Maker or Editor modules.
* '''Single File''' read only the selected file to form a volume. By default, matching sequences of 2D image files are assembled into a volume. For example, in a directory containing image001.png, image002.png, and image003.png, if Single File us unchecked then selecting image001.png will put all three images together into a volume. Checking Single File will result in just image001.png being loaded as a single-slice volume.

==== Recent Volumes ====

This menu shows the most recent volumes you have loaded. Selecting an entry will browse to the directory where the file is stored and will restore the Volume Options settings that were in place when the file was loaded.

=== Add Data ===

[[Image:AddData.png|thumb|300px|right|The Add Data dialog]]

For general purpose data loading, slicer offers the File->Add Data... dialog which allows bulk loading of the contents of entire directories.

==== Add Directory ====
[[Image:SelectDirectory.png|thumb|200px|right|The Select Directory dialog]]

This brings up a dialog that allows you to select a directory containing data you wish to load. You may optionally select a pattern of file names to match. By default, this is * which matches all files. You may wish to use something like *.nii or patient1.* for example. By default the selected directory and all subdirectories will be searched; unchecking the Recurse checkbox will limit the search to only the selected directory.

==== Add File(s) ====

This button brings up a standard file browse dialog. You can select a single file or multiple files to add to the load list.

==== Data List ====

*'''Select''' If checked then this file will be loaded (use this to suppress unwanted files that may have been added by Add Directory)
*'''File''' The file name. This is editable if you want to specify a different file.
*'''Type''' This data type as determined by the file extension.
*'''Name''' The name that will appear in slicer. By default it is the filename minus the extension. You can edit this field to choose a different name.
*'''Label Map''' (Applies to Volumes only) Volume should be treated as a label map.
*'''Centered''' (Applies to Volumes only) Volume should be centered around 0,0,0.

==== List Management Options ====

*'''Clear Entries''' Remove all entries from the Data List
*'''Select All''' Select all entries for loading
*'''Select None''' Unselect all entries
*'''Label All''' (Applies to Volumes only) Mark all volumes as label maps
*'''Label None''' (Applies to Volumes only) Mark all volumes as non-label maps
*'''Centered All''' (Applies to Volumes only) Center all volumes
*'''Centered None''' (Applies to Volumes only) Do not center any volumes

==== Data Types ====

Data types are determined based on the following file extensions:

*'''Volumes''' .hdr .nhdr .nrrd .mhd .mha .vti .nii .gz .mgz
*'''Models'''.vtk .vtp .g .stl .orig .inflated .sphere .white .smoothwm .pial
*'''QDEC Project files''' .qdec
*'''XCEDE Catalog files''' .xcat
*'''Fiducial Lists''' .fcsv

===Known bugs===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker.

===Usability issues===

Follow this [http://na-mic.org/Mantis/main_page.php link] to the Slicer3 bug tracker. Please select the '''usability issue category''' when browsing or contributing.

==Use Cases==
*I have dicom files on a memory stick
Copy them into a folder on your system. Open from there. For general information about loading data into Slicer, click [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training here] and select tutorial 1.1
*Subscenarios
**CT
**MRI
**PET
**DTI
**DCE
**fMRI
*I have Freesurfer results
**Look at our Freesurfer tutorial. Click [http://wiki.na-mic.org/Wiki/index.php/Slicer3.2:Training here] and select tutorial 1.8
*I have a data set in Analyze format
*I have a volumetric jpeg
*I have a sequence of 2d jpeg images
*I have a FITS data set

← Older revision		Revision as of 13:57, 10 June 2010
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	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]		[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]
		+
		+	[[Modules:Loading-Data-3.6#Loading_DICOM_Image_Data \| Return to Loading DICOM Volume Data Documentation]]

	[[Modules:Loading-Data-3.6#Adding_Scalar_and_Tensor_Volumes\|Return to Loading Scalar and Tensor Volume Data Documentation]]		[[Modules:Loading-Data-3.6#Adding_Scalar_and_Tensor_Volumes\|Return to Loading Scalar and Tensor Volume Data Documentation]]

@@ Line 25: / Line 25: @@
 The Path field can be used to quickly get to a directory or file, for example if you want to paste in a directory path from another window.
-Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.
+Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.18].
 ==== DICOM Files ====

@@ Line 25: / Line 25: @@
 The Path field can be used to quickly get to a directory or file, for example if you want to paste in a directory path from another window.
-Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.6].
+Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.
 ==== DICOM Files ====

@@ Line 25: / Line 25: @@
 The Path field can be used to quickly get to a directory or file, for example if you want to paste in a directory path from another window.
-Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.10].
+Slicer 3.6 can read the file types supported by [http://www.itk.org ITK version 3.6].
 ==== DICOM Files ====

← Older revision		Revision as of 13:35, 10 June 2010
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	[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]		[[Documentation-3.6\|Return to Slicer 3.6 Documentation]]
−	[[Loading ~~Tractography~~-3.6\|Return to Loading ~~Tractography~~ Data Documentation]]	+
		+	[[Modules:Loading-Data-3.6#Adding_Scalar_and_Tensor_Volumes\|Return to Loading Scalar and Tensor Volume Data Documentation]]

DICOMBrowser-3.6 - Revision history

Wjp at 13:57, 10 June 2010

Wjp: /* Non-DICOM Files */

Wjp: /* Volumes */

Wjp: /* Volumes */

Wjp: /* Volumes */

Wjp at 13:35, 10 June 2010

Wjp: Created page with 'Return to Slicer 3.6 Documentation Return to Loading Tractography Data Documentation __NOTOC__ == General Information == ===…'

Wjp: Created page with 'Return to Slicer 3.6 Documentation Return to Loading Tractography Data Documentation NOTOC == General Information == ===…'