Trouble reading a DICOM MRI series

Operating system: Windows 7
Slicer version: 4.5, 4.8
Expected behavior: Reads in DICOM MRI series as a single volume
Actual behavior: Reads each image into an individual volume


This MRI series is not being read in as a volume. Each image is being put into an individual volume. Any ideas on what’s going on and how to fix it?

These slices are not combined because the DICOM headers report they are from different studies (0020,000d) and from different series (0020,000e). I would check the providence of these images, and see if you can get earlier copies of the images before these tags were manipulated.

Based on 0002,0013, I suspect these images were mangled by a Matlab script (potentially attempting to anonymize data). The DICOM format is extremely complex, and this makes DICOM images fragile to manipulation. Personally, I am a fan of gdcmanon.

(0002,0013) SH [MATLAB IPT 7.1] # 14, 1 ImplementationVersionName

Instance Number 1:

(0020,000d) UI [] #  64, 1 StudyInstanceUID
(0020,000e) UI [] #  64, 1 SeriesInstanceUID

Instance Number 2:

(0020,000d) UI [] #  64, 1 StudyInstanceUID
(0020,000e) UI [] #  64, 1 SeriesInstanceUID

Hmm - interesting. I get the same behavior with the original non-anonomized images. They are from another site, so I don’t know about how they were obtained.

I can try changing the DICOM fields in Matlab. Would changing (0020,000d) and (0020,000e) be enough for Slicer?

I could also try saving them in another format (nrrd, nifti?). I would need to save the spatial information.


That fixed it.

Thanks again!