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

[Jonathan Harlap]

My first suggestion would be to use dcm2mnc instead of dicom3_to_minc,
given that dicom3_to_minc isn't being worked on anymore and dcm2mnc
handles a lot of scanner-specific weirdnesses that dicom3_to_minc
doesn't.

Cheers,
J

On Wed, Apr 30, 2008 at 10:03 AM, Audette, Michel
<Michel.Audette at medizin.uni-leipzig.de> wrote:
> 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
>
>
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>