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Remember to save your resultant dataset as Nifti or NRRD. Once it is loaded, you can cross reference the metadata (namely image dimensions and spacing) from MorphoSource to the values reported by the Volume module. Once DICOM browser completes the import, you should now have a record called Saimiri_201870000.dcm click on it and hit load. Notice how slow it is now importing (as it should, this is a massive 3GB dataset). Once patching is completed, you can use the DICOM browser to import the patched dataset. #Download slicer 3d data seriesThis will recreate the DICOM series in the specified folder. Make sure Generate missing patient/study/series ID is checked and hit Patch. To fix this problem, open the DICOM Patcher module, specify Saimiri_20187 folder as the DICOM Input, and choose an output folder. It complains about dataset missing the patient and study name, as well as an Unknown DICOM tag. If you scroll down, you should see error messages labeled critical. We can dig further on the root cause of the problem by hitting CTRL+0 and bringing the Log Messages dialog box. Slicer will begin loading the DICOM series, and eventually will display a message saying 0 Patient/Studies/Series were imported. This is really a moot point, as in the end we will save the dataset as NRRD or NII, which are far more suitable for our purposes than image sequences. If you choose the latter, and later change or remove the location of Saimiri_20187 folder, you won’t be able to reload your data. You can either choose to incorporate the DICOM sequence into the DICOM database or simply link the files. Open the DICOM module, Click Import and navigate a few folders down to the Saimiri_20187 folder, and hit OK. #Download slicer 3d data zip fileThe solution here is based on the response from the Andras Lasso (Thanks Andras!).ĭownload the zip file (1.9GB) and unzip it to a folder. ![]() ![]() I also chose MorphoSource, because recently a user had issues getting the data into Slicer. #Download slicer 3d data registrationRegistration is well worth the hassle, as it provides thousands of scanned vertebrate specimens in a very nicely curated manner. #Download slicer 3d data downloadYou may have to register for the site to download the data. ![]() For the ones that fail, DICOM patcher can be used to strip the meta data portion of DICOM and just load the image.įor this tutorial, I will use a DICOM series from the excellent MorphoSource repository ( ). It should read almost all well-structured DICOM series. ![]() Slicer has a robust DICOM import/export module. While it is a standard, manufacturers of imaging equipment implemented the format in different ways, which can be a amajor headache. DICOM is a standard image data format that is designed to facilitate data exchange between medical imaging facilities. ![]()
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