Trouble reading a DICOM MRI series

Support
1

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

Hi,

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?

2

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 [1.3.6.1.4.1.9590.100.1.2.380037498713055046739759443493873218136] #  64, 1 StudyInstanceUID
(0020,000e) UI [1.3.6.1.4.1.9590.100.1.2.331408360012808881138554615400916651736] #  64, 1 SeriesInstanceUID

Instance Number 2:

(0020,000d) UI [1.3.6.1.4.1.9590.100.1.2.222023342810310160709387564850599174001] #  64, 1 StudyInstanceUID
(0020,000e) UI [1.3.6.1.4.1.9590.100.1.2.385511264811362958821958401890266751484] #  64, 1 SeriesInstanceUID
3

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.

Thanks,
Nathan

4

That fixed it.

Thanks again!