[MINC-users] dcm2mnc error, seems related to slice position/orientation
Audette, Michel
Michel.Audette at medizin.uni-leipzig.de
Wed Apr 30 10:44:14 EDT 2008
Hi again,
in any event, dcm2mnc winges with this particular data set:
maudette at icaw164201:~/data/data/Dyna_CT> dcm2mnc Kann/*.IMA Kann_mnc/ -clob -verbose
Checking file types...
File Kann/KANN.OT.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.1000.1.2008.04.21.13.58.31.718750.1245303.IMA appears to be DICOM (CD/Export).
WARNING: Failed to find image position
...
WARNING: Failed to find image position
Using 482 files
Sorting 482 files...
num filename studyid serialno acq nec iec ndy idy nsl isl acol rcol mrow img# seq
0 4.21.13.54.58.187500.1214558.IMA 20080420.090629 55032 1 -1 -1 -1 1 1 -1 -1 1024 -1 300
... (bunch of lines like this)
481 4.21.13.58.31.718750.1245323.IMA 20080420.090629 11532 1000 -1 -1 -1 -1 -1 -1 -1 128 -1 2
Done sorting files.
Processing files, one series at a time...
Using directory 'Kann_mnc/'
file_prefix: [Kann_mnc/]
Series 1 Kann Fluoro Card Klappen2 ( 2 files):
Kann/KANN.XA.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.1.300.2008.04.21.13.54.58.187500.1214558.IMA
Kann/KANN.XA.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.1.301.2008.04.21.13.54.58.187500.1214593.IMA
WARNING: Image coordinates absent or incomplete.
WARNING: Slice location is untrustworthy.
WARNING: Failed to find image orientation!
Using default direction cosines
WARNING: Can't find pixel size element
0. Slice axis length 1
1. Echo axis length 1
2. Time axis length 1
3. Phase axis length 1
4. ChmSh axis length 1
0. Z axis length 1 step -1.000, start -1.000, cosines -0.000,-0.000,1.000
1. Y axis length 1024 step -1.000, start 0.000, cosines -0.000,1.000,-0.000
2. X axis length 1024 step -1.000, start 0.000, cosines 1.000,-0.000,-0.000
SOP Class UID: 1.2.840.10008.5.1.4.1.1.12.1
Images in acquisition: 1
Acquisitions in series: -1
3D raw partitions: -1
Pixel minimum 0.0000000000 maximum 4095.0000000000
Window minimum 0.0000000000 maximum 4096.0000000000
WARNING: Failed to find image orientation!
Using default direction cosines
WARNING: Can't find pixel size element
Directory Kann_mnc/kann_20080421_090629 exists...
MINC file name: Kann_mnc/kann_20080421_090629/kann_20080421_090629_1.mnc
Patient name: Kann
Study ID: 20080420.090629
Acquisition ID: 1
Registration date: 20080421
Registration time: 090629.015000
Rows 1024 columns 1024 slices 1/1
Writing 2 images to MINC file
Created minc file Kann_mnc/kann_20080421_090629/kann_20080421_090629_1.mnc.
Series 2 Kann Fluoro Card Klappen2 ( 1 files):
Kann/KANN.XA.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.2.100.2008.04.21.13.54.58.187500.1214628.IMA
WARNING: Image coordinates absent or incomplete.
WARNING: Failed to find image orientation!
Using default direction cosines
WARNING: Can't find pixel size element
WARNING: Failed to find image position
0. Slice axis length 1
1. Echo axis length 1
2. Time axis length 1
3. Phase axis length 1
4. ChmSh axis length 1
0. Z axis length 1 step -1.000, start 1.000, cosines -0.000,-0.000,1.000
1. Y axis length 1024 step -1.000, start 0.000, cosines -0.000,1.000,-0.000
2. X axis length 1024 step -1.000, start 0.000, cosines 1.000,-0.000,-0.000
SOP Class UID: 1.2.840.10008.5.1.4.1.1.12.1
Images in acquisition: 1
Acquisitions in series: -1
3D raw partitions: -1
Pixel minimum 0.0000000000 maximum 4095.0000000000
Window minimum 750.0000000000 maximum 3450.0000000000
Directory Kann_mnc/kann_20080421_090629 exists...
MINC file name: Kann_mnc/kann_20080421_090629/kann_20080421_090629_2.mnc
Patient name: Kann
Study ID: 20080420.090629
Acquisition ID: 2
Registration date: 20080421
Registration time: 090629.015000
Rows 1024 columns 1024 slices 1/1
Writing 1 images to MINC file
Created minc file Kann_mnc/kann_20080421_090629/kann_20080421_090629_2.mnc.
Series 3 Kann 5s-1k DR ( 465 files):
Kann/KANN.OT.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.3.1.2008.04.21.13.54.58.187500.625726.IMA
... (bunch of lines like this)
Kann/KANN.XA.CORONARY_DIAGNOSTIC_CORONARY_CATHETERIZATION.3.222.2008.04.21.13.54.58.187500.635182.IMA
WARNING: Image coordinates absent or incomplete.
WARNING: Slice location is untrustworthy.
WARNING: Failed to find image orientation!
Using default direction cosines
WARNING: Can't find pixel size element
0. Slice axis length 1
1. Echo axis length 1
2. Time axis length 1
3. Phase axis length 1
4. ChmSh axis length 1
0. Z axis length 1 step -1.000, start -1.000, cosines -0.000,-0.000,1.000
1. Y axis length 1024 step -1.000, start 0.000, cosines -0.000,1.000,-0.000
2. X axis length 1024 step -1.000, start 0.000, cosines 1.000,-0.000,-0.000
SOP Class UID: 1.2.840.10008.5.1.4.1.1.12.1
Images in acquisition: -1
Acquisitions in series: -1
3D raw partitions: -1
Pixel minimum 0.0000000000 maximum 4095.0000000000
Window minimum 0.0000000000 maximum 4096.0000000000
WARNING: Failed to find image orientation!
WARNING: Failed to find image position
WARNING: No image position found
... (skipping info again)
Mismatched rows/columns, marking invalid
WARNING: Inconsistent pixel minimum and maximum
0.000000 4095.000000, 0.000000 65535.000000
Mismatched rows/columns, marking invalid
WARNING: Coordinate spacing (1) differs from DICOM slice spacing (-1)
(perhaps you should consider the -usecoordinates option)
Using -1 for the slice spacing value.
Directory Kann_mnc/kann_20080421_090629 exists...
MINC file name: Kann_mnc/kann_20080421_090629/kann_20080421_090629_3.mnc
Patient name: Kann
Study ID: 20080420.090629
Acquisition ID: 3
Registration date: 20080421
Registration time: 090629.015000
Rows 1024 columns 1024 slices 133/133
Writing 465 images to MINC file
WARNING: Failed to find image orientation!
WARNING: Failed to find image position
WARNING: No image position found
WARNING: Failed to find image position
WARNING: Failed to find image orientation!
WARNING: Failed to find image position
WARNING: No image position found
WARNING: Failed to find image position
Segmentation fault
ends with this fault.
Thanks again for your kind consideration.
Best regards,
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
-----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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