I have a number of patients of whom I have DICOM files of T1w-MRI and rCBV maps pre-and postop. For most patients these load just fine, as scalar volumes as they should. However for some, it only gives the option to load as an Image Sequence, which leaves me with single slice with 19 iterations.
When I open this sequence in the Sequences module, it wil let me play and it will literally just present all 19 slices in order, so the data is there… The data before importing into 3DSlicer does not look any different at all to another rCBV maps that loads just fine; a DICOM file and the folders with 19 images.
It seems to me that some of the data is “corrupted”, in that it thinks it is a 1 slice sequence with 19 iterations, instead of 19 slices that need to be stacked.
If it helps, I could make a video to explain a bit better what is going on.
TLDR: Some of my scalar volumes only allow loading as Image Sequence, Is there any way to edit something under the hood of this DICOM (or in 3DSlicer) that can rectify this? Thank you very much in advance.
To add, I have noticed that in properties it says that the Image Dimension is 256x256x1 times 19 (1 being the Z axis and 19 being the time axis). This is what should be 256x256x19 times 1, which it is for the ones that work.
There are many DICOM representations of data
that users may want to see as volumes or sequences in Slicer. We try to handle most of them but not all patterns are easy to detect. The best solution would be for you to look at the headers and the sequence and volume dicom plugin python code
and find the patterns that apply to your data and propose extensions that would handle the data in the way you need it. I know this may sound complicated, but if you know what the data is meant to represent and you know something about the acquisition it’s probably straightforward.
Hi Steve, thanks for your input. I’ve gotten pretty handy with basic 3DSlicer but these kind of problems still stump me. I’ll take a look at your proposed solution and let you know if I make progress!
