[MINC-users] dicom3_to_minc error, seems related to slice position/orientation
Audette, Michel
Michel.Audette at medizin.uni-leipzig.de
Wed Apr 30 10:32:31 EDT 2008
Hi Jonathan,
sorry about that... I probably should have noted this before. I'll rename my dicom3_to_minc to something else, or delete it altogether.
Cheers,
Michel
-----Original Message-----
From: minc-users-bounces at bic.mni.mcgill.ca on behalf of Jonathan Harlap
Sent: Wed 4/30/2008 4:25 PM
To: MINC users mailing list
Subject: Re: [MINC-users] dicom3_to_minc error,seems related to slice position/orientation
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
>
>
> _______________________________________________
> MINC-users at bic.mni.mcgill.ca
> http://www2.bic.mni.mcgill.ca/mailman/listinfo/minc-users
>
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