Combination of 2 series with interslice gaps, acquired in an interleaved manner

Operating system: Windows 10
Slicer version: 4.10.2
Expected behavior:
Actual behavior:

Hello 3D slicer community.
I have 2 2D MRI series, acquired in an interleaved manner.
Namely, 1 series is acquired in a 1.2mm slice thickness with 1.2mm gap, and the other series with the same dimension, but slighted shifted to acquire slices in the location of the gaps, in the first series.
I want to stich them into 1 series, however when I load them on 3D slicer, and add them, it results in 2.4-mm slice thickness images.
I want to make the 2 series into a 1.2mm slice thickness series, but cannot figure out a way.
I kindly ask for your help.

Best wishes,
Ho-Joon Lee

One approach could be to patch DICOM files before importing, so that all the files are read as a single series. Probably overwriting Series Instance UID would be enough. You can use DCMTK’s dcmodify command-line tool or pydicom Python package.

Another approach would be to merge the two stacks after loading the volumes. Probably the easiest is to get the volumes as 3D numpy arrays, merge the arrays using standard numpy operations, and set the merged array into a volume node.

Thank you Andras for your comments.

I have tried to patch the DICOM files with the tool in 3D slicer, but when imported with the DICOM tool, it recognizes the patched DICOM series as 2 separate series.
Is there some other way to do it in Slicer?
For the second suggesting, I am not really familiar with the Slicer API, is there a tutorial that I might follow?


Slicer’s DICOM Patcher module does not change existing series instance UID in a DICOM file. You need to write your own script to do that.

See programming tutorials on the Slicer training page. Mostly those two functions that I’ve posted the links to should be the Slicer-specific functions you need.