[MINC-users] dicom3_to_minc error, seems related to slice position/orientation

[Audette, Michel]

Hi folks, 

sorry to make a nuisance of myself these days. I'm confronting dicom3_to_minc errors once again: 

maudette at icaw164201:~/data/data/Dyna_CT> dicom3_to_minc Kust_mnc/ Kust/*IMA
Reading headers from file "Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.102.2008.04.29.10.16.22.890625.796180.IMA"
************** Error reading slice position ***************
************* Error reading slice orientation *************
... (a bunch more like this)
Reading headers from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.10.1.2008.04.29.10.16.22.890625.1702044.IMA"
************** Error reading slice position ***************
************* Error reading slice orientation *************
Creating minc file "Kust_mnc//k_st_martin_1_013013_mri.mnc"
Duplicate slice position: ignoring file Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.110.2008.04.29.10.16.22.890625.796193.IMA
Duplicate slice position: ignoring file Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.118.2008.04.29.10.16.22.890625.796206.IMA
Duplicate slice position: ignoring file Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.1.2008.04.29.10.16.22.890625.795985.IMA
... (a few more like this)
Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.86.2008.04.29.10.16.22.890625.796154.IMA
Duplicate slice position: ignoring file Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.9.2008.04.29.10.16.22.890625.795998.IMA
Duplicate slice position: ignoring file Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.94.2008.04.29.10.16.22.890625.796167.IMA
Getting data from file "Kust/K_ST_MARTIN.OT.CARD_KLAPPEN.13.102.2008.04.29.10.16.22.890625.796180.IMA" for slice 0.
(from micreate_group_variable): Variable 'dicom_0x0002' is not a standard MINC variable
micreate_group_variable: MINC package entry point
... (a few more like this)
(from micreate_group_variable): Variable 'dicom_0x0040' is not a standard MINC variable
micreate_group_variable: MINC package entry point
Reading headers from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.1.100.2008.04.29.10.16.22.890625.799240.IMA"
Creating minc file "Kust_mnc//k_st_martin_1_010010_mri.mnc"
Getting data from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.10.1.2008.04.29.10.16.22.890625.1702044.IMA" for slice 0.
(from micreate_group_variable): Variable 'dicom_0x0002' is not a standard MINC variable
micreate_group_variable: MINC package entry point
... (a few more like this)
(from micreate_group_variable): Variable 'dicom_0x5000' is not a standard MINC variable
micreate_group_variable: MINC package entry point
Reading headers from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.1.101.2008.04.29.10.16.22.890625.799255.IMA"
...
Reading headers from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.11.1.2008.04.29.10.16.22.890625.1702201.IMA"
************** Error reading slice position ***************
************* Error reading slice orientation *************
Creating minc file "Kust_mnc//k_st_martin_1_001001_mri.mnc"
Getting data from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.1.10.2008.04.29.10.16.22.890625.797890.IMA" for slice 0.
Using blank image for slice 1 (:).
... (same message for slices 2-87)
Using blank image for slice 88 (:).
Using blank image for slice 89 (:).
Getting data from file "Kust/K_ST_MARTIN.XA.CARD_KLAPPEN.1.100.2008.04.29.10.16.22.890625.799240.IMA" for slice 90.
G

The end result is a bunch of minc files featuring large blank subvolumes. 

Can anyone suggest a course of action? 

Cheers, 

Michel

Michel Audette, Ph.D.
Innovation Center Computer Assisted Surgery (ICCAS)
Semmelweisstraße 14
Leipzig, Germany
Phone: ++49 (0) 341 / 97 - 1 20 13
Fax: ++49 (0) 341 / 97 - 1 20 09