How to read DICOMDIR file

Hi, I’ve got DTI data using Siemens 3T MRI scanner, and ti si DICOMDIR format. I use MiscroDIcom software to open it, and I get images from different series

and I want to transfer them into different DICOM files according to the series, which is the function of the software.
Then I used MrTrix3 to see the info of the dcm files using mrinfo. And I got this error:
So it seems like the MiscroDicom’s function is not perfect? Or something.
Anyone one knowes how to solve this? Any tools support my thought, you know, transfer the DICOMDIR to multiplt DICOM files

Welcome @BarryLiu97!

I’ve no experience with the software itself, but I’ll at least chime in with a couple of observations:

  • The software claims that the “original” image size is 1024x1024. This means that the input DWIs are almost certainly stored in a mosaic format. I don’t know whether or not that tool will preserve the information regarding the mosaic storage as it passes from input to output, but it’s something to pay attention to.

  • Normally a DICOM dataset is a directory, containing multiple files with the .dcm extension. Whereas here it looks like you’re opening a directory whose name ends with “.dcm”. It’s likely that you specified the output directory name yourself, but included “.dcm” in the path. It’ll still work, but for your own sanity I’d suggest leaving “.dcm” out of directory paths to avoid confusion.

  • You can check the contents of individual DICOM files, rather than the entire dataset, using the dcminfo command. That might yield more specific information about what data are there (and not there). For instance, if ignoring the stacked-slice mosaic nature of the original DICOMs and just writing a single large mosaic image per DWI volume, slice position information would not be necessary, so the image data “are still there” but can’t be interpreted as a set of 3D volumes.

  • While I don’t know the nuances of the distinction between “DICOMDIR” and DICOM, have you tried simply bypassing that software entirely and loading the original data into MRtrix3?


Hi, I’ve solved this. I used mrconvert successfully convert DICOMDIR to nii. It would show me all the series of MRI and I just need to choose that with the number.