Hello,
I am encountering a strange issue while reconstructing a T1-weighted image from a 3T GE scanner, especially since I have been processing other subjects with exactly the same protocol and had no problem. Here is the command I used and its output:
Dimon -infile_prefix MR -gert_create_dataset -save_details DET
Dimon version 4.26 (February 3, 2020) running, use to quit…
– scanning for first volume
++ DICOM WARNING: Slice_Spacing=0.500001 smaller than Slice_Thickness=1.000000
++ Setting environment variable AFNI_SLICE_SPACING_IS_GAP ++
++ to YES will make the center-to-center slice distance ++
++ be set to Slice_Spacing+Slice_Thickness= 1.500. ++
++ This is against the DICOM standard [attribute (0018,0088) ++
++ is defined as the center-to-center spacing between slices, ++
++ NOT as the edge-to-edge gap between slices], but it seems ++
++ to be necessary for some GE scanners. ++
++ ++
++ This correction has been made on this data: dz= 1.500. ++
++ ++
++ Setting AFNI_SLICE_SPACING_IS_GAP to NO means that the ++
++ DICOM Slice_Spacing variable will be used for dz, replacing ++
++ the Slice_Thickness variable. This usage may be required ++
++ for some pulse sequences on Phillips scanners. ++
++ Data detected to be oblique
++ DICOM WARNING: Slice_Spacing=0.500001 smaller than Slice_Thickness=1.000000
++ DICOM WARNING: no more Slice_Spacing messages will be printed
– writing file list to DET…
first_read : – writing file list to DET…
first_sort : – writing details to DET.1.first_sort.txt…
.
** no_wait: no volume found in 344 files
– writing file list to DET…
no_vol : – writing details to DET.2.no_vol.txt…
I’d be happy to send the details files output by Dimon (it seems I cannot attach them here)
Thanks in advance for any suggestions
giuseppe