Documentation/Nightly/FAQ/DICOM - Revision history

Lasso: Moved to read-the-docs

2020-11-02T19:13:37Z

Moved to read-the-docs

Lasso: /* I try to import a directory of DICOM files, but nothing shows up in the browser */

2019-10-16T14:29:08Z

I try to import a directory of DICOM files, but nothing shows up in the browser

ChrisR: /* I try to import a directory of DICOM files, but nothing shows up in the browser */

2019-09-21T16:56:06Z

I try to import a directory of DICOM files, but nothing shows up in the browser

Lasso: /* Something is displayed, but it is not what I expected */

2019-04-11T17:40:51Z

Something is displayed, but it is not what I expected

Lasso: /* Image is stretched or compressed along one axis */

2019-04-09T18:04:37Z

Image is stretched or compressed along one axis

Lasso: /* Image is stretched or compressed along one axis */

2019-04-09T18:03:17Z

Image is stretched or compressed along one axis

Lasso: /* Something is displayed, but it is not what I expected */

2019-04-09T18:00:36Z

Something is displayed, but it is not what I expected

Lasso: /* I try to import a directory of DICOM files, but nothing shows up in the browser */

2019-03-22T23:04:28Z

I try to import a directory of DICOM files, but nothing shows up in the browser

Lasso: /* I try to import a directory of DICOM files, but nothing shows up in the browser */

2018-12-30T03:10:50Z

I try to import a directory of DICOM files, but nothing shows up in the browser

Lasso: /* I try to import a directory of DICOM files, but nothing shows up in the browser */

2018-11-13T23:25:57Z

I try to import a directory of DICOM files, but nothing shows up in the browser

@@ Line 1: / Line 1: @@
-<noinclude>{{documentation/versioncheck}}</noinclude>
+<noinclude>{{documentation/versioncheck}}
-<noinclude>__TOC__
+</noinclude>
-==What is DICOM anyway?==
+{{documentation/banner
+| text  = [{{documentation/{{documentation/version}}/slicer-manual-base-url}}/user_guide/modules/dicom.html This page has been moved to read-the-docs.]
-Digital Imaging and Communications in Medicine (DICOM) is the standard for the communication and management of medical imaging information and related data (see Wikipedia article [https://en.wikipedia.org/wiki/DICOM here]). Among other things, DICOM defines format of objects for communicating images and image-related data. In most cases, imaging equipment (CT and MR scanners) used in the hospitals will generate images saved as DICOM objects.
+| background-color = 8FBC8F }}

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 * Make sure the Slicer temporary folder is writeable. Temporary folder can be selected in menu: Edit / Application Settings / Modules / Temporary directory.
 * Try moving the data and the database directory to a path that includes only US English characters (ASCII) to avoid possible parsing errors. No special, international characters are allowed.
 * To confirm that your installation of Sicer is reading data correctly, try loading other data, such as [https://s3.amazonaws.com/IsomicsPublic/SampleData/QIN-HEADNECK-01-0024-CT.zip this anonymized sample DICOM series (CT scan)]
 * Try import using different DICOM readers: in Application settings / DICOM / DICOMScalarVolumePlugin / DICOM reader approach: switch from DCMTK to GDCM (or GDCM to DCMTK), restart Slicer, and attempt to load the data set again.

@@ Line 46: / Line 46: @@
 * To confirm that your installation of Sicer is reading data correctly, try loading other data, such as [https://s3.amazonaws.com/IsomicsPublic/SampleData/QIN-HEADNECK-01-0024-CT.zip this anonymized sample DICOM series (CT scan)]
 * Try import using different DICOM readers: in Application settings / DICOM / DICOMScalarVolumePlugin / DICOM reader approach: switch from DCMTK to GDCM (or GDCM to DCMTK), restart Slicer, and attempt to load the data set again.
-* Try the [https://github.com/lassoan/SlicerDicomPatcher DICOM Patcher]  module
+* See if the SlicerDcm2nii extension will convert your images. You can install this module using the Extension manager. Once installed you will be able to use the Dcm2niixGUI module from slicer.
 * Review the [[Documentation/{{documentation/version}}/SlicerApplication/ErrorLog|Error Log]] for information.
 * Try loading the data by selecting one of the files in the [[Documentation/{{documentation/version}}/SlicerApplication/LoadingData|Add Data Dialog]].  ''Note: be sure to turn on Show Options and then turn off the Single File option in order to load the selected series as a volume''
-* If you are still unable to load the data, you may need to find a utility that converts the data into something Slicer can read.  Sometimes tools like [http://surfer.nmr.mgh.harvard.edu/ FreeSurfer], [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ FSL] or [http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html MRIcron] can understand special formats that Slicer does not handle natively.  These systems typically export [http://nifti.nimh.nih.gov/nifti-1/ NIfTI] files that slicer can read.
+* If you are still unable to load the data, you may need to find a utility that converts the data into something Slicer can read.  Sometimes tools like [http://surfer.nmr.mgh.harvard.edu/ FreeSurfer], [http://fsl.fmrib.ox.ac.uk/fsl/fslwiki/ FSL] or [https://www.nitrc.org/projects/mricron MRIcron] can understand special formats that Slicer does not handle natively.  These systems typically export [http://nifti.nimh.nih.gov/nifti-1/ NIfTI] files that slicer can read.
-* If you are sure that the DICOM files do not contain patient confidential information, you may post a sample dataset on a web site and ask for help from [https://discourse.slicer.org Slicer forum].  ''Please be careful not to accidentally reveal private health information''.  If you want to remove identifiers from the DICOM files you may want to look at [http://www.dclunie.com/pixelmed/software/webstart/DicomCleanerUsage.html DicomCleaner] or [http://mircwiki.rsna.org/index.php?title=CTP-The_RSNA_Clinical_Trial_Processor the RSNA Clinical Trial Processor] software.
+* For archival studies, are you sure that your data is in DICOM format, or is it possible the data is stored in one of the proprietary [http://www.dclunie.com/medical-image-faq/html/part4.html MR] or [http://www.dclunie.com/medical-image-faq/html/part3.html CT] formats that predated DICOM? If the latter, you may want to try the dcm2nii tool distributed with [https://www.nitrc.org/frs/?group_id=152 MRIcron] up until 2016. More recent versions of MRIcorn include dcm2niix, which is better for modern DICOM images. However, the legacy dcm2nii includes support for proprietary formats from GE, Philips, Siemens and Elscint.
 == Something is displayed, but it is not what I expected ==

← Older revision		Revision as of 17:40, 11 April 2019
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	Scanners may create image volumes with varying image slice spacing. Slicer can represent such images in the scene by apply a non-linear transform. To enable this feature, go to menu: Edit / Application settings / DICOM and set ''Acquisition geometry regularization'' to ''apply regularization transform''. Slice view, segmentation, and many other features work directly on non-linearly transformed volumes. For some other features, such as volume rendering, you need to harden the transform on the volume: go to Data module, in the row of the volume node, double-click on the transform column, and choose ''Harden transform''.		Scanners may create image volumes with varying image slice spacing. Slicer can represent such images in the scene by apply a non-linear transform. To enable this feature, go to menu: Edit / Application settings / DICOM and set ''Acquisition geometry regularization'' to ''apply regularization transform''. Slice view, segmentation, and many other features work directly on non-linearly transformed volumes. For some other features, such as volume rendering, you need to harden the transform on the volume: go to Data module, in the row of the volume node, double-click on the transform column, and choose ''Harden transform''.
		+
		+	Note that if Slicer displays a warning about non-uniform slice spacing then it may be due to missing or corrupted DICOM files. There is no reliable mechanism to distinguish between slices that are missing because they had not been acquired (for example, to reduce patient dose) or they were acquired but later they were lost.

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 === Image is stretched or compressed along one axis ===
-Some non-clinical (industrial or pre-clinical) imaging systems do not generate valid DICOM data sets. For example, they may incorrectly assume that slice thickness tag defines image geometry, while according to DICOM standard, image slice position must be used for determining image geometry. ''DICOM Patcher'' module can fix some of these images: remove the images from Slicer's DICOM database, process the image files with DICOM Patcher module, and re-import the processed file into Slicer's DICOM database.
+Some non-clinical (industrial or pre-clinical) imaging systems do not generate valid DICOM data sets. For example, they may incorrectly assume that slice thickness tag defines image geometry, while according to DICOM standard, image slice position must be used for determining image geometry. ''DICOM Patcher'' module can fix some of these images: remove the images from Slicer's DICOM database, process the image files with DICOM Patcher module, and re-import the processed file into Slicer's DICOM database. If image is still distorted, go to ''Volumes'' module, open ''Volume information'' section, and adjust ''Image spacing'' values.
 Scanners may create image volumes with varying image slice spacing. Slicer can represent such images in the scene by apply a non-linear transform. To enable this feature, go to menu: Edit / Application settings / DICOM and set ''Acquisition geometry regularization'' to ''apply regularization transform''. Slice view, segmentation, and many other features work directly on non-linearly transformed volumes. For some other features, such as volume rendering, you need to harden the transform on the volume: go to Data module, in the row of the volume node, double-click on the transform column, and choose ''Harden transform''.

@@ Line 41: / Line 41: @@
 If you have trouble importing DICOM data here are some steps to try:
 * Make sure you are following the [[Documentation/{{documentation/version}}/Modules/DICOM|DICOM]] module documentation.
-* Try using the latest nightly build of Slicer.
+* We are constantly improving the application (new preview version is released every day), so there is a chance that the problem you encountered is addressed in a recent version. Try loading the data using the latest stable and the latest nightly versions of Slicer.
 * Make sure the Slicer temporary folder is writeable. Temporary folder can be selected in menu: Edit / Application Settings / Modules / Temporary directory.
 * Try moving the data and the database directory to a path that includes only US English characters (ASCII) to avoid possible parsing errors. No special, international characters are allowed.