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Itk metaimage to dicom
Itk metaimage to dicom




itk metaimage to dicom
  1. ITK METAIMAGE TO DICOM INSTALL
  2. ITK METAIMAGE TO DICOM CODE
  3. ITK METAIMAGE TO DICOM SERIES

But I agree that it would be better if you got a more clear indication of error, such as returning an error code or throw an exception. Not creating a file at all is a robust way of indicating that something went wrong and SimpleITK may also log errors or set error codes somewhere. You need to generate new UIDs for some fields, while cross-referencing existing UIDs in other fields.

itk metaimage to dicom itk metaimage to dicom

You need to provide lots of required metadata to have a chance of generating a valid DICOM file. And if I am doing something wrong, then I feel that I at least deserve some kind of notice like: “ERROR: We disabled writing DICOM because !”.Ĭreation of valid DICOM files is very complex and not done very often.

itk metaimage to dicom

Overall, this is a very frustrating situation, because I had written a script that outputs DICOM files using SimpleITK (I am converting some MHDs to DICOM for further processing), and since SimpleITK is a part of Slicer, I assumed that I could run it in Slicer. ShNode.SetItemParent(volumeShItemID, studyItemID)Įxporter = DICOMScalarVolumePlugin.DICOMScalarVolumePluginClass()Įxportables = exporter.examineForExport(volumeShItemID) VolumeShItemID = shNode.GetItemByDataNode(volumeNode) StudyItemID = shNode.CreateStudyItem(patientItemID, "test study") PatientItemID = shNode.CreateSubjectItem(shNode.GetSceneItemID(), "test patient") # Create patient and study and put the volume under the study The only script example for exporting an image as DICOM is this, which starts with object types I don’t recognize and uses a bunch of functionality I was hoping to avoid: volumeNode = getNode("CTChest")

ITK METAIMAGE TO DICOM SERIES

mhd/.raw file pair to a DICOM series (I have the tags stored separately)?Ĭan someone please consider adding an error message to be printed when SimpleITK.WriteImage() fails? Is there a good way to export a SimpleITK image object as DICOM from Slicer? Or more generally to convert an. Has anyone else used SimpleITK ImageFileWriter/WriteImage to write DICOM files from Slicer scripts? Is there a way to fix the problem? Now I am afraid I will have to rewrite the script in order to use Slicer’s internal DICOM modules, which will require a few days of reading, probably.

ITK METAIMAGE TO DICOM INSTALL

The script works perfectly on my laptop with a standalone SimpleITK library, but on my work desktop I cannot install standalone SimpleITK (ugh) so I thought I would try to run it inside of Slicer, which I am allowed to install. And if I am doing something wrong, then I feel that I at least deserve some kind of notice like: “ERROR: We disabled writing DICOM because !”. # using sitk.ImageFileWriter().Execute() gives the same behavior, incidentally Sitk.WriteImage(slices, "C:\\Users\\username\\test\\0000.dcm") # does nothing, gives no error message, just does nothing Sitk.WriteImage(slices, "C:\\Users\\username\\test\\0000.nrrd") # works fine Sitk.WriteImage(slices, "C:\\Users\\username\\test\\0000.mhd") # works fine save (save_path + '/' + str (i ) + '.Here’s what’s happening (at the Slicer Python console): import SimpleITK as sitk fromarray (scan ) #Here is the extracted image data Make_dir (save_path ) for i in range (scan. shape ) #Image size print ( 'spacing: ', spacing ) #interval print ( '# slice: ', len (scan ) ) #Number of slices #plot_ct_scan(scan) GetArrayFromImage (data ) print ( 'scan.shape' ,scan. join (root ,path ) ) #Read mhd file #print(data) Plot = plots if num_row = 1 else plots ĭata =sitk. subplots (num_row, num_column, figsize = (num_column * 5, num_row * 5 ) ) for i in range ( 0, num_row *num_column ) : Num_row = (num_slices //jump + num_column - 1 ) // num_columnį, plots = plt. makedirs (save_path ) #Integrate all pictures of a patient into one picture and print it out def plot_ct_scan (scan, num_column = 4, jump = 1 ) : #Create empty directory def make_dir (save_path ) : if not os. #Get the name of the subfolder in the file def get_file_name (filename ) : for root, dirs, files in os. My data storage is roughly as follows E:/105casesMask_Seg is the total data folder, the Cxxx folder stores the mhd files of each patient, the file name is equivalent to the patient_name later #Import the required package import os






Itk metaimage to dicom