Documentation/Nightly/Modules/DICOM - Revision history

Lasso: Moved to readthedocs

2020-11-02T19:02:07Z

Moved to readthedocs

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Lasso: /* DICOM export */

2020-06-02T14:09:42Z

DICOM export

Pieper: /* Advanced options */

2020-03-07T15:30:28Z

Advanced options

Lasso: Added notes that installing extensions may help with import/export

2019-11-26T16:00:29Z

Added notes that installing extensions may help with import/export

Show changes

Pinter: /* DICOM export */

2019-07-26T12:34:46Z

DICOM export

Pinter: /* Customize DICOM browser table content */

2019-05-08T16:28:30Z

Customize DICOM browser table content

Lasso: /* Slicer DICOM Database */

2019-05-01T20:54:22Z

Slicer DICOM Database

Lasso at 20:17, 28 April 2019

2019-04-28T20:17:54Z

Lasso at 20:16, 28 April 2019

2019-04-28T20:16:43Z

Show changes

Pinter: /* Customize table columns in DICOM browser */

2019-04-16T16:08:42Z

Customize table columns in DICOM browser

@@ Line 118: / Line 118: @@
 Referring to the "DICOM in use" image in the top left of this page, the most important controls for day-to-day use are highlighted with gray callouts.  The are described here in the order you are likely to use them.
-*'''LocalDatabase''' (appears when ''>>'' button next to the menu bar is clicked): allows you to select a location on disk for Slicer's database of DICOM files. The application manages content of this folder (stores metadata and copy of imported DICOM files): do not manually copy any data into this folder.
+Basic options:
 *'''Import''' all DICOM files in the selected folder (including subfolders) will be parsed and basic information from file headers will be stored in Slicer's DICOM database. If enabled, then Slicer will make a copy of the imported files into the database folder.
 *'''Patient list''' shows patients in the database. Studies available for the selected patient(s) are listed in study list. Multiple patients can be selected.
 *'''Study list''': shows studies for the currently selected patient(s).  Multiple studies can be selected.
 *'''Series list''' shows list of series (images, structure sets, segmentations, registration objects, etc.) available for selected studies.
-*'''Search boxes''' Each patient/study/series can be filtered by typing in these fields.
+*'''Load''' click this to load currently selected loadables into slicer.
 *'''Examine button''' Runs each of the DICOM Plugins on the currently selected series and offers the result in the Load Options table.
 *'''Loadables list''' displays all possible interpretations of the selected series by the selected plugins.  The plugin that most likely interprets the series correctly, is selected by default.  You can override the defaults if you want to load the data in a different way. There will not always be a one-to-one mapping of selected series to list of loadable items.
-*'''Load''' click this to load currently selected loadables into slicer.
-*'''Metadata''' click this button to see metadata stored in file headers of selected series.
+DICOM module settings:
 ==DICOM export==
@@ Line 183: / Line 201: @@
 *Open DICOM browser
-*Select the data set that you want to load by clicking on a series (item in the listbox in the bottom)
+*Right-click on the data set that you want to inspect
-*Click Metadata button
+*Choose "View DICOM metadata"
 *Click Copy Metadata button
 *Paste the copied text to any text editor

@@ Line 159: / Line 159: @@
 **Scalar Volume
 ***You can choose what back-end library to use (currently GDCM, DCMTK, or GDCM with DCMTK fallback with the last option being the default.  This is provided in case some data is unsupported by one library or the other.
-***Acquisition geometry regularization option supports the creation of a nonlinear transform that corrects for things like missing slices or gantry tilt in the acquisition
+***Acquisition geometry regularization option supports the creation of a nonlinear transform that corrects for things like missing slices or gantry tilt in the acquisition.  See [https://github.com/Slicer/Slicer/commit/b7650af3c27f34fc894bfdd587f2a4c02ba62a8b this commit message for more information]
 ***Autoloading subseries by time is an option break up some 4D acquisitions into individual volume, but is optional since some volumes are also acquired in time unites and should not be split.

@@ Line 64: / Line 64: @@
 Data in the scene can be exported to the DICOM database:
-* Right-click on a data set in Data module (subject hierarchy tab) to export it to DICOM format. Export can also be initiated from DICOM browser.
+* Prepare DICOM study to export in Data module (subject hierarchy tab). Make sure you have the nodes in the study that you want to export.
 * Edit tags for exportables. The metadata from the select study will be automatically filled in to the Export dialog and you can select a Slicer volume to export.
 * Exported files are added to the DICOM database

@@ Line 218: / Line 218: @@
 The fields are [https://github.com/commontk/CTK/9c2af28e84da1abb986036317d75009d4c149923/blob/master/Libs/DICOM/Core/ctkDICOMDatabase.h#L207 updated] when 1) files are added to the database or 2) the database schema is updated (happens when opening an older database with a newer Slicer). In the [https://github.com/commontk/CTK/tree/9c2af28e84da1abb986036317d75009d4c149923 current] version only those files (i.e. instances) are processed for which the displayed fields have never been generated.
-When updating the displayed fields, every rule defines the fields it is responsible for using the cached DICOM tags in the database. Tags can be requested to be cached in the rules from the [https://github.com/commontk/CTK/blob/9c2af28e84da1abb986036317d75009d4c149923/Libs/DICOM/Core/ctkDICOMDisplayedFieldGeneratorAbstractRule.h#L63 getRequiredDICOMTags] function. New field values are generated by the rules instance by instance. First, the getDisplayedFieldsForInstance function is called for each rule in which the custom values are generated from the raw tags, then the results are merged by calling mergeDisplayedFieldsForInstance for all the rules. Each field can requested to be merged with "expect same value", which uses the only non-empty value and throws a warning if conflicting values are encountered, or with "concatenate", which simply concatenates the displayed field values together.
+When updating the displayed fields, every rule defines the fields it is responsible for using the cached DICOM tags in the database. Tags can be requested to be cached in the rules from the [https://github.com/commontk/CTK/blob/9c2af28e84da1abb986036317d75009d4c149923/Libs/DICOM/Core/ctkDICOMDisplayedFieldGeneratorAbstractRule.h#L63 getRequiredDICOMTags] function. New field values are generated by the rules instance by instance. First, the getDisplayedFieldsForInstance function is called for each rule in which the custom values are generated from the raw tags, then the results are merged by calling mergeDisplayedFieldsForInstance for all the rules. Each field can be requested to be merged with "expect same value", which uses the only non-empty value and throws a warning if conflicting values are encountered, or with "concatenate", which simply concatenates the displayed field values together.
 The existing two rules can be used as examples: the [https://github.com/commontk/CTK/blob/9c2af28e84da1abb986036317d75009d4c149923/Libs/DICOM/Core/ctkDICOMDisplayedFieldGeneratorDefaultRule.cpp default] and the [https://github.com/commontk/CTK/blob/9c2af28e84da1abb986036317d75009d4c149923/Libs/DICOM/Core/ctkDICOMDisplayedFieldGeneratorRadiotherapySeriesDescriptionRule.cpp RT] rules.

← Older revision		Revision as of 20:54, 1 May 2019
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	To organize the data and avoid redundant calculations, Slicer keeps a DICOM Database of information about the DICOM data. You can have multiple databases on your computer at a time, and switch between them if, for example, they include data from different research projects. Each database is simply a directory on your local disk that has a few [http://sqlite.org/ SQLite] files and subdirectories to store image data. Don't manually modify the contents of these directories. DICOM data can enter the database either through manual import or via a DICOM network transfer. Modules may also populate the DICOM database with the results of computation.		To organize the data and avoid redundant calculations, Slicer keeps a DICOM Database of information about the DICOM data. You can have multiple databases on your computer at a time, and switch between them if, for example, they include data from different research projects. Each database is simply a directory on your local disk that has a few [http://sqlite.org/ SQLite] files and subdirectories to store image data. Don't manually modify the contents of these directories. DICOM data can enter the database either through manual import or via a DICOM network transfer. Modules may also populate the DICOM database with the results of computation.
		+
		+	You can change location where the database is stored by opening the DICOM module, clicking the double arrow (>>) button on the right side of the menu bar, click the button next to "LocalDatabase" label, and select the new location (an empty folder).

	Note that the DICOM standard does not specify how files will be organized on disk, so if you have DICOM data from a CDROM or otherwise transferred from a scanner, you cannot in general tell anything about the contents from the file or directory names. However once the data is imported to the database, it will be organized according the the DICOM standard Patient/Study/Series hierarchy.		Note that the DICOM standard does not specify how files will be organized on disk, so if you have DICOM data from a CDROM or otherwise transferred from a scanner, you cannot in general tell anything about the contents from the file or directory names. However once the data is imported to the database, it will be organized according the the DICOM standard Patient/Study/Series hierarchy.

@@ Line 27: / Line 27: @@
 {{documentation/{{documentation/version}}/module-description}}
-DICOM is a widely used and sophisticated set of standards for digital radiology (see the [[#References|References]] section for more information). Slicer provides support for a subset of DICOM functionality, with the particular features driven by the needs of clinical research: '''loading''' and '''saving''' data sets from/to disk in DICOM format or '''receiving''' data sets via DICOM networking.
+DICOM is a widely used and sophisticated set of standards for digital radiology (see the [[#References|References]] section for more information). Slicer provides support for a subset of DICOM functionality, with the particular features driven by the needs of clinical research: '''loading''' and '''saving''' data sets from/to disk in DICOM format and '''sending''' and '''receiving''' data sets via DICOM networking.
 <!-- ---------------------------- -->

← Older revision		Revision as of 16:08, 16 April 2019
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	Columns in the browser can be renamed, reordered, shown/hidden, etc. An example snippet to customize the browser can be found in the [https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Customize_table_columns_in_DICOM_browser script repository]		Columns in the browser can be renamed, reordered, shown/hidden, etc. An example snippet to customize the browser can be found in the [https://www.slicer.org/wiki/Documentation/Nightly/ScriptRepository#Customize_table_columns_in_DICOM_browser script repository]
		+
		+	The changes made like this are written into the database (ColumnDisplayProperties table), so the column customizations can be done only once per database.

	==== Customize DICOM browser table content ====		==== Customize DICOM browser table content ====