Problem with Dimon

AFNI Message Board
1

Dear AFNI experts,

I am using Dimon to convert DICOMS to nifti. I normally use the following code to convert Phillips DICOMs.


Dimon -infile_pattern 'IM_*' -GERT_Reco -quit -use_last_elem -use_slice_loc -dicom_org -sort_by_acq_time -gert_write_as_nifti

For some reason I am having issues with this subject in particular and I am not sure about the cause of that.
Could someone help me converting these files and telling me what could be wrong?

Here are the DICOMs
… edited …

Thanks in advance,
Karel

2

Hi Karel,

All of the acquisition times in the Dicom files seem to be the same, so that is not a great sorting technique here. To evaluate the sorting, use something like “-save_details DET”, which will save a few DET* text files, showing what is influencing the sorting.

These files, as I see is noted in the Dimon help output, seem to be sorted (according to the common REL Instance Number) in slice-major order, meaning all images for slice 0 come first, then all for slice 1, and continued over time. So a better way to go might be use use that natural ordering, and add the -order_as_zt option.

For example, this seems to work with your data:

Dimon -infile_pattern 'data/IM_*'                    \
      -gert_create_dataset -use_last_elem -dicom_org \
      -order_as_zt save_det DET

Unless specified, -dicom_org uses the REL instance number for sorting (see the “RIN” column of the DET files), which works here, after flipping the time and z positions with -order_as_zt.

Give that a try and see how it goes.

  • rick