Interrupted GE 4D scans not converted properly into a 4D NIfTI file

[cmadjar]

Describe the bug

Interrupted DWI or BOLD images acquired on GE scanners fail conversion into a 4D NIfTI file. Instead, it creates a 3D file with dimensions xyz 14x140x5280.

To reproduce

I was able to reproduce the error by deleting the last few DICOM files of a GE 4D acquisition. Not sure if this reproduces exactly the problem we see with the interrupted file but might be worth trying it on your end to reproduce the bug and find a fix. We are working on getting example data we could share but it might take a while before we are able to provide test data.

Command run: dcm2niix -b na -z y -o <nifti_dir> <dicom_dir>

Expected behavior

When trying to convert the image, the last partial frame resulting from the interrupted scan should be ignored to create the 4D NIfTI files with the rest of the complete frames.

Output log

Chris Rorden's dcm2niiX version v1.0.20230904  (JP2:OpenJPEG) (JP-LS:CharLS) GCC9.4.0 x86-64 (64-bit Linux)
Found 5373 DICOM file(s)
DICOM images may be missing, expected 87 spatial locations per volume, but found 5373 slices.
Slice positions repeated, but number of slices (5373) not divisible by number of repeats (62): missing images?
Hint: expected 87 locations
Warning: Instance Number (0020,0013) order is not spatial.
Error: Check sorted order: 4D dataset has 1 volumes, but volume index ranges from 30720..30806
Warning: Interslice distance varies in this volume (incompatible with NIfTI format).
Error: Missing images. Found 5373 images, expected 87 slices per volume and instance number (0020,0013) ranges from 1 to 5394
Convert 5373 DICOM as niftis/dicoms_HBCD_MainStudy_v1.2_20251015140046_4a (140x140x5373x1)
Unable to equalize slice distances: slice order not consistently ascending:
dx=[0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 1.7 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 3.39999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 5.09999 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137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 137.7 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 139.4 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 141.1 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 142.8 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 144.5 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2 146.2]
 Recompiling with '-DmyInstanceNumberOrderIsNotSpatial' might help.

Version

Chris Rorden's dcm2niiX version v1.0.20230904  (JP2:OpenJPEG) (JP-LS:CharLS) GCC9.4.0 x86-64 (64-bit Linux)

Note: this particular version has been built out of the commit c5caaa9f_20230921 which fixed a similar issue we had with Philips scanners

Troubleshooting

• Does the latest stable release resolve your issue?

Unfortunately no

• Does the latest commit on the development branch resolve your issue?

Unfortunately no

[neurolabusc]

This is the intended behavior. Most DICOM images do not explicitly report the number of files, and it is unclear how the user wants to proceed with a partial volume. It is easy to use ChatGPT to write a python script to try to delete partial volumes, but this seems to be something the user should do under full knowledge that some of the data is being discarded. The variation between vendors in handling partial volumes also likely complicates features - in particular in my experience Philips instance numbers are rarely sequential with temporal acquisition order.