We recently upgraded our Siemens Prisma from the VE11E to XA30 operating system. Our dicom header format has also changed with XA30. I use Dimon to reconstruct our data, which still works fine for single volume datasets. However, Dimon is having trouble with multi-volume datasets (e.g. EPI scans). Each dicom should have 60 slices, but Dimon is only finding the first slice of each volume, then crashing because it expects 60 slices per volume but only finds the first.
[As an aside, I used Matlab's dicominfo and dicomread to study the files. Our EPI scan has a matrix size of 90x90. Our VE11E dicoms were saved as mosaic format, but the XA30 dicoms are saved as a matrix: 90x90x1x60.]
Reading the Dimon help, it appears Dimon only works for single-slice volumes or mosaic volumes. Is there a work-around, or plan to expand Dimon to include non-mosaic multislice volumes? A work-around would help in the short-term for offline processing, but we also use Dimon for real-time fMRI studies, so expanding Dimon to cover the XA30 dicom header system would be ideal for long-term.
As an example, I tried using Dimon to reconstruct the first 10 images of my EPI scan. Here's my command and output.
Dimon -infile_pattern '*.dcm' -gert_create_dataset -gert_outdir ./ -gert_to3d_prefix test
Dimon version 4.29 (February 16, 2022) running, use to quit...
-- scanning for first volume
++ Data detected to be oblique
** CID: have non-mosaic 00001.dcm with 60 images
*+ WARNING: Bad DICOM header - assuming oblique scaling direction!
** CID: have non-mosaic 00002.dcm with 60 images
no more warnings will be printed...
-- first volume found (1 slices)
-- scanning for additional volumes...
-- run 11: 1 2 3 4 5 6 7 8 9 10
final run statistics:
volume info :
slices : 1
z_first : -30.79
z_last : -30.79
z_delta : 2.4
oblique : yes
mos_nslices : 0
run # 11 : volumes = 10, first file (#0) = 00001.dcm
++ writing dimon file list to dimon.files.run.011
** warning: oblique data, consider -use_obl_origin
set OutlierCheck =
set OutDir = ./
test -d ./
to3d -prefix test.sdmt -time:zt 1 10 0.8sec alt+z -@
++ to3d: AFNI version=AFNI_22.1.02 (Apr 6 2022) [64-bit]
++ Authored by: RW Cox
++ It is best to use to3d via the Dimon program.
++ Counting images: total=600 2D slices
** Number of slices on command line = 600
** Number of slices needed for -time: = 10
** Something is wrong with your command line!
mv: No match.