The series reader does not sort the list of files, the files are read in the order they are specified. The SimpleITK ImageSeriesReader it the class which handles a list of files when passes to sitk.ReadImage. Sitk.WriteImage(image,os.path.join(output_folder,acc,series_desc+'_'+value+'.nii.gz')) Print ('-> Writing image:', series_desc+'_'+value) Print ('-> Fundamental error in image layer, skipping.') #Group Common Series File Paths By Time Acquistion Os.mkdir(os.path.join(output_folder,acc))įor i,value in enumerate(unique_column_values): If os.path.exists(os.path.join(output_folder,acc)) = True: # Check and Make Study Folder if Does Not Exist

dcm file paths should be made into a series-specific 3D data setĭef nifti_by_series(unique_column_values,column_number,dicom_table,output_folder): #Then I use the unique list generated in the first block to inform SimpleITK which groups of. dcm files, how does “reader.SetFileNames()” know what order to write/stack them in? Are there specific DICOM tags I’m neglecting that can be leveraged to preprocess before sending them to “reader.SetFileNames()”?Īny suggestions or guidance is greatly appreciated.

This helped with some initial issues, but not the ones described above. dcm by “acquisition time” and “series description” and/or “series ID” before feeding to “reader.SetFileNames()”. Series = #list of dicom file paths with common acquisition time and series description Also, what should be the ends of the data sometimes appear in the middle, like a frame shift. I’m hoping someone else here has crossed this bridge before and may be able to share advice.įor example, there can be random few slices from the chest that suddenly appear in the abdomen (probably the images that were used for bolus timing). The approach I’m using is below and works great, BUT for some of the data the slices are not in the correct order due to something specific to the scanner might be writing to the meta data. I’m trying to convert a CT abdomen triple-phase dicom data folder into nifti 3D data by series.

Osirix lite nifti to dicom