I'm not sure it's the conversion, but I checked the metadata for the dicom and it should be one single volume. Does anyone know how to keep it as one volume during conversion? Or just simply merge the two volumes together to get one? As it is now, loading it into a program that doesn't allow you to choose which volume to view defaults to the lower half of the head (I assume since it's the first one in the array) but I need the entire head.
The problem is not with dcm2niix, but your images. One set does not have the transfer syntax set - this is a Type 1 property, so these are not longer valid DICOMs. The second case has been corrupted with variable slice instance UIDs. In both cases, I think you can fix this by working out the providence of these images and getting copies prior to corruption.
For the second case, dcm2niix clearly warns you:
slices not stacked: series instance UID varies (duplicates all other properties)
You could try to salvage your data with this the "-m y":
dcm2niix -m y -f %t_%s_%p ~/tst/NITRC
But you will need to make sure that you only process one exam at a time.
Your DICOMs have been corrupted: each slice from a single 2D series has been assigned a different StudyInstanceUID, e.g.
(0020,000d) UI [1.3.6.1.4.1.11157.2018.9.10.17.12.50.6714] # 42, 1 StudyInstanceUID
I suggest you check the providence of your images and see where they were corrupted. While I have never heard of "MultiTech msiCOM", this would be my prime suspect.
(0002,0013) SH [MultiTech msiCOM] # 16, 1 ImplementationVersionName
Originally posted by Rita Chen:
I have an MRI study with a single patient and series as dicom images but for some reason when I convert to Nifti with dmc2niix it gets split into 2 volumes. I tried opening it with MRIcroGL to check and it looks like it's been split into the lower and upper half of the head. (this is still just a single .nii file with two volumes, not that it was output as two separate .nii files). I'm not sure it's the conversion, but I checked the metadata for the dicom and it should be one single volume. Does anyone know how to keep it as one volume during conversion? Or just simply merge the two volumes together to get one? As it is now, loading it into a program that doesn't allow you to choose which volume to view defaults to the lower half of the head (I assume since it's the first one in the array) but I need the entire head.
Hi Rita,
Did you find a solution to your problem?
I have the same problem with a 3D acquisition from a GE scanner.
I'm sure it is not a problem with DICOMS as those are directly
obtained from the scanner, so no chance of corrupting the
DICOMs.
Thanks,
Alexey.
Alexey,
Your question is underspecified, but I am going to guess that you acquired data using GE's Zip2 interpolation and converted with an obsolete version of dcm2niix that was not aware of this technique. You should make sure your are using the latest version (v1.0.20230411):
https://github.com/rordenlab/dcm2niix/releases
You can see the version as the first line of output each time you run dcm2niix.
Chris Rorden's dcm2niiX version v1.0.20230411 Clang14.0.3 ARM (64-bit MacOS)
In general, I would discourage using interpolation at the acquisition stage. I would expect the image will get resliced during spatial normalization.
How to get slices of single DICOM file. I have a dataset that contains numerous DICOM files, and each DICOM file contain 30 slices. I want PNG/JPG of each slice that is 30 slices (PNG/JPG) from single DICOM file. How to get it?