I have 60 DICOM files, each of them is one slice with all the timeframes (x,y,1,timeframes). I want to get (x,y,60,timeframes) but I can't seem to get it working. Siemens machine

Output is: Chris Rorden's dcm2niiX version v1.0.20250330  (JP2:OpenJPEG) (JP-LS:CharLS) MSC1942  (64-bit Windows)
Found 60 DICOM file(s)

Let me make sure I understand the question. You have DICOM images from a Siemens scanner that is saved as mosaics:

  https://nipy.org/nibabel/dicom/dicom_mos...

However, dcm2nii is failing to detect them. There are two issues:

 1. Data comes from a Siemens V* MRI software (e.g. VE11). In this case, the mosaic information is stored in the CSA header, and failure to detect this suggests the CSA headers have been stripped from your DICOM. The solution is to search the provenance of your DICOMs and convert images prior to the removal of these tags (which also provide critical sequence infromation). I suspect an anonymization stage removed these details.

   https://nipy.org/nibabel/dicom/siemens_csa.html

 2. Data was acquired using Siemens XA MRI software (e.g. XA30). In this case, the mosaic images are for visual inspection only, and do not contain the information required to analyze the data (e.g. slice timing, gradient information, etc). In this case, you will want to re-export the data from your scanner without the mosaic mode. In my experience, these mosaics lack Type 1 (required) information, so they are not actually valid DICOM images, rather they are DICOM data files. They are too impoverished for reproducible science.

  https://github.com/rordenlab/dcm2niix/is...

The Siemens Research Collaboration Manager affiliated with your center can aid you in these steps.

Thank you for your response, but I don't think I have mosaic images. My situation is different and specifically involves 4D flow MRI data:

1. I have 60 separate DICOM files from a Siemens scanner (XA60)
   
2. Each file represents a different slice position (so 60 different slice positions)
   
3. Each file contains all the timeframes for its specific slice position (4D flow acquisition)
   

What I'm trying to do is merge these 60 files into a single 4D volume where:

• The first 3 dimensions are spatial (x, y, 60 slices)


• The 4th dimension is temporal (all timeframes)

When I run dcm2niix, it finds the 60 files but doesn't seem to complete the conversion process. 

Perhaps you can share the entire series with my institutional email

https://sc.edu/study/colleges_schools/artsandsciences/psychology/our_people/directory/rorden_chris.php

I do think you want to work with the Siemens Research Collaboration Manager to see why each file contains all the timepoints for one slice, rather than all the slices for one timepoint. I have never seen this before and the behavior seems atypical. You may also want to export images directly off the scanner prior to it being touched by other devices to ensure that this modification did not happen at another stage (it does seem like OFFIS_DCMTK_354 touched these files).

You may also want to see if anyone at SNUG has seen this - I do not have local access to XA60, so I am not sure what setting elicited this behavior.
  https://www.snug-discuss.org/