Re: [Freesurfer] Re: zero determinant error in using mri_convert rawavg.mgz orig.mgz --conform

looks like it thinks the slice thickness is 0, which is probably bad.... On Wed, 13 May 2009, Nick Schmansky wrote:

John,

What does the file look like when its opened in tkmedit? ie

tkmedit -f T1.mgz

does it look like our sample subject data bert? ie, a full brain t1 anatomical scan?

Nick

On Wed, 2009-05-13 at 16:41 -0400, John Drozd wrote:

...

    Hello,

    Here is the ouput from bugr:

    FREESURFER_HOME: /trumpet/downloads/FreeSurfer/freesurfer

    Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v4.3.0

    RedHat release: Fedora release 10 (Cambridge)

    Kernel info: Linux 2.6.27.21-170.2.56.fc10.x86_64 x86_64

    I have sets of dicom files such as:

    [jdrozd@trumpet orig]$ ls
    70731171155016_S32496_I63397_0.dcm*
     70731171155016_S32496_I63397_25.dcm*
    70731171155016_S32496_I63397_100.dcm*
     70731171155016_S32496_I63397_26.dcm*
    70731171155016_S32496_I63397_101.dcm*
     70731171155016_S32496_I63397_27.dcm*
    70731171155016_S32496_I63397_102.dcm*
     70731171155016_S32496_I63397_28.dcm*
    70731171155016_S32496_I63397_103.dcm*
     70731171155016_S32496_I63397_29.dcm*
    70731171155016_S32496_I63397_104.dcm*
     70731171155016_S32496_I63397_2.dcm*
    70731171155016_S32496_I63397_105.dcm*
     70731171155016_S32496_I63397_30.dcm*
    70731171155016_S32496_I63397_106.dcm*
     70731171155016_S32496_I63397_31.dcm*
    70731171155016_S32496_I63397_107.dcm*
     70731171155016_S32496_I63397_32.dcm*
    70731171155016_S32496_I63397_108.dcm*
     70731171155016_S32496_I63397_33.dcm*
    70731171155016_S32496_I63397_109.dcm*
     70731171155016_S32496_I63397_34.dcm*
    70731171155016_S32496_I63397_10.dcm*
    70731171155016_S32496_I63397_35.dcm*
    70731171155016_S32496_I63397_110.dcm*
     70731171155016_S32496_I63397_36.dcm*
    70731171155016_S32496_I63397_111.dcm*
     70731171155016_S32496_I63397_37.dcm*
    70731171155016_S32496_I63397_112.dcm*
     70731171155016_S32496_I63397_38.dcm*
    70731171155016_S32496_I63397_113.dcm*
     70731171155016_S32496_I63397_39.dcm*
    70731171155016_S32496_I63397_114.dcm*
     70731171155016_S32496_I63397_3.dcm*
    70731171155016_S32496_I63397_115.dcm*
     70731171155016_S32496_I63397_40.dcm*
    70731171155016_S32496_I63397_116.dcm*
     70731171155016_S32496_I63397_41.dcm*
    70731171155016_S32496_I63397_117.dcm*
     70731171155016_S32496_I63397_42.dcm*
    70731171155016_S32496_I63397_118.dcm*
     70731171155016_S32496_I63397_43.dcm*
    70731171155016_S32496_I63397_119.dcm*
     70731171155016_S32496_I63397_44.dcm*
    70731171155016_S32496_I63397_11.dcm*
    70731171155016_S32496_I63397_45.dcm*
    70731171155016_S32496_I63397_120.dcm*
     70731171155016_S32496_I63397_46.dcm*
    70731171155016_S32496_I63397_121.dcm*
     70731171155016_S32496_I63397_47.dcm*
    70731171155016_S32496_I63397_122.dcm*
     70731171155016_S32496_I63397_48.dcm*
    70731171155016_S32496_I63397_123.dcm*
     70731171155016_S32496_I63397_49.dcm*
    70731171155016_S32496_I63397_124.dcm*
     70731171155016_S32496_I63397_4.dcm*
    70731171155016_S32496_I63397_125.dcm*
     70731171155016_S32496_I63397_50.dcm*
    70731171155016_S32496_I63397_126.dcm*
     70731171155016_S32496_I63397_51.dcm*
    70731171155016_S32496_I63397_127.dcm*
     70731171155016_S32496_I63397_52.dcm*
    70731171155016_S32496_I63397_128.dcm*
     70731171155016_S32496_I63397_53.dcm*
    70731171155016_S32496_I63397_129.dcm*
     70731171155016_S32496_I63397_54.dcm*
    70731171155016_S32496_I63397_12.dcm*
    70731171155016_S32496_I63397_55.dcm*
    70731171155016_S32496_I63397_130.dcm*
     70731171155016_S32496_I63397_56.dcm*
    70731171155016_S32496_I63397_131.dcm*
     70731171155016_S32496_I63397_57.dcm*
    70731171155016_S32496_I63397_132.dcm*
     70731171155016_S32496_I63397_58.dcm*
    70731171155016_S32496_I63397_133.dcm*
     70731171155016_S32496_I63397_59.dcm*
    70731171155016_S32496_I63397_134.dcm*
     70731171155016_S32496_I63397_5.dcm*
    70731171155016_S32496_I63397_135.dcm*
     70731171155016_S32496_I63397_60.dcm*
    70731171155016_S32496_I63397_136.dcm*
     70731171155016_S32496_I63397_61.dcm*
    70731171155016_S32496_I63397_137.dcm*
     70731171155016_S32496_I63397_62.dcm*
    70731171155016_S32496_I63397_138.dcm*
     70731171155016_S32496_I63397_63.dcm*
    70731171155016_S32496_I63397_139.dcm*
     70731171155016_S32496_I63397_64.dcm*
    70731171155016_S32496_I63397_13.dcm*
    70731171155016_S32496_I63397_65.dcm*
    70731171155016_S32496_I63397_140.dcm*
     70731171155016_S32496_I63397_66.dcm*
    70731171155016_S32496_I63397_141.dcm*
     70731171155016_S32496_I63397_67.dcm*
    70731171155016_S32496_I63397_142.dcm*
     70731171155016_S32496_I63397_68.dcm*
    70731171155016_S32496_I63397_143.dcm*
     70731171155016_S32496_I63397_69.dcm*
    70731171155016_S32496_I63397_144.dcm*
     70731171155016_S32496_I63397_6.dcm*
    70731171155016_S32496_I63397_145.dcm*
     70731171155016_S32496_I63397_70.dcm*
    70731171155016_S32496_I63397_146.dcm*
     70731171155016_S32496_I63397_71.dcm*
    70731171155016_S32496_I63397_147.dcm*
     70731171155016_S32496_I63397_72.dcm*
    70731171155016_S32496_I63397_148.dcm*
     70731171155016_S32496_I63397_73.dcm*
    70731171155016_S32496_I63397_149.dcm*
     70731171155016_S32496_I63397_74.dcm*
    70731171155016_S32496_I63397_14.dcm*
    70731171155016_S32496_I63397_75.dcm*
    70731171155016_S32496_I63397_150.dcm*
     70731171155016_S32496_I63397_76.dcm*
    70731171155016_S32496_I63397_151.dcm*
     70731171155016_S32496_I63397_77.dcm*
    70731171155016_S32496_I63397_152.dcm*
     70731171155016_S32496_I63397_78.dcm*
    70731171155016_S32496_I63397_153.dcm*
     70731171155016_S32496_I63397_79.dcm*
    70731171155016_S32496_I63397_154.dcm*
     70731171155016_S32496_I63397_7.dcm*
    70731171155016_S32496_I63397_155.dcm*
     70731171155016_S32496_I63397_80.dcm*
    70731171155016_S32496_I63397_156.dcm*
     70731171155016_S32496_I63397_81.dcm*
    70731171155016_S32496_I63397_157.dcm*
     70731171155016_S32496_I63397_82.dcm*
    70731171155016_S32496_I63397_158.dcm*
     70731171155016_S32496_I63397_83.dcm*
    70731171155016_S32496_I63397_159.dcm*
     70731171155016_S32496_I63397_84.dcm*
    70731171155016_S32496_I63397_15.dcm*
    70731171155016_S32496_I63397_85.dcm*
    70731171155016_S32496_I63397_160.dcm*
     70731171155016_S32496_I63397_86.dcm*
    70731171155016_S32496_I63397_161.dcm*
     70731171155016_S32496_I63397_87.dcm*
    70731171155016_S32496_I63397_162.dcm*
     70731171155016_S32496_I63397_88.dcm*
    70731171155016_S32496_I63397_163.dcm*
     70731171155016_S32496_I63397_89.dcm*
    70731171155016_S32496_I63397_164.dcm*
     70731171155016_S32496_I63397_8.dcm*
    70731171155016_S32496_I63397_165.dcm*
     70731171155016_S32496_I63397_90.dcm*
    70731171155016_S32496_I63397_16.dcm*
    70731171155016_S32496_I63397_91.dcm*
    70731171155016_S32496_I63397_17.dcm*
    70731171155016_S32496_I63397_92.dcm*
    70731171155016_S32496_I63397_18.dcm*
    70731171155016_S32496_I63397_93.dcm*
    70731171155016_S32496_I63397_19.dcm*
    70731171155016_S32496_I63397_94.dcm*
    70731171155016_S32496_I63397_1.dcm*
     70731171155016_S32496_I63397_95.dcm*
    70731171155016_S32496_I63397_20.dcm*
    70731171155016_S32496_I63397_96.dcm*
    70731171155016_S32496_I63397_21.dcm*
    70731171155016_S32496_I63397_97.dcm*
    70731171155016_S32496_I63397_22.dcm*
    70731171155016_S32496_I63397_98.dcm*
    70731171155016_S32496_I63397_23.dcm*
    70731171155016_S32496_I63397_99.dcm*
    70731171155016_S32496_I63397_24.dcm*
    70731171155016_S32496_I63397_9.dcm*

    I first converted these files to an mgz file using:

    [jdrozd@trumpet orig]$ mri_convert -it dicom
    70731171155016_S32496_I63397_0.dcm T1.mgz
    mri_convert -it dicom 70731171155016_S32496_I63397_0.dcm
    T1.mgz
    $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
    reading from 70731171155016_S32496_I63397_0.dcm...
    Starting DICOMRead2()
    dcmfile
    = /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm
    dcmdir
    = /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig
    WARNING: tag ImageNumber not found
    Ref Series No = 63443
    Found 168 files, checking for dicoms
    WARNING: tag ImageNumber not found
    Found 166 dicom files in series.
    WARNING: tag ImageNumber not found
    First Sorting
    WARNING: files are not found to be different and cannot be
    sorted
    File1: /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_0.dcm
    File2: /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri/orig/70731171155016_S32496_I63397_1.dcm
    Computing Slice Direction
    Vs: 1.2024 0 0
    Vs: 1 0 0
    Second Sorting
    Counting frames
    nframes = 1
    nslices = 166
    ndcmfiles = 166
    PE Dir = UNKNOWN (dicom read)
    TransferSyntaxUID: --1.2.840.10008.1.2--
    jpegUID:           --1.2.840.10008.1.2.4--
    Loading pixel data
    TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    i_ras = (-0, -0, -1)
    j_ras = (-0, -1, 0)
    k_ras = (-1, -0, 0)
    writing to T1.mgz...

    Then I copied the outputted T1.mgz file using:

    [jdrozd@trumpet orig]$ cp T1.mgz ../rawavg.mgz
    [jdrozd@trumpet orig]$ cd ..
    [jdrozd@trumpet mri]$ ls
    1.Bvq.Xml*  2.Bvq.Xml*  error.log  orig/  orig2/  rawavg.mgz
     transforms/
    [jdrozd@trumpet mri]$ pwd
    /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri

    Then I tried to conform the data using:

    [jdrozd@trumpet mri]$ mri_convert rawavg.mgz orig.mgz --
    conform
    mri_convert rawavg.mgz orig.mgz --conform
    $Id: mri_convert.c,v 1.146.2.4 2009/01/30 02:30:42 nicks Exp $
    reading from rawavg.mgz...
    TR=0.00, TE=0.00, TI=0.00, flip angle=0.00
    i_ras = (-0, -0, -1)
    j_ras = (-0, -1, 0)
    k_ras = (-1, -0, 0)
    Original Data has (0.93905, 0.93905, 0) mm size and (256, 256,
    166) voxels.
    Data is conformed to 1 mm size and 256 voxels for all
    directions
    changing data type from 4 to 0 (noscale = 0)...
    MRIchangeType: Building histogram
    Reslicing using trilinear interpolation
    MRIresample(): source matrix has zero determinant; matrix is:
    -0.000  -0.000  -0.000   0.000;
    -0.000  -0.939  -0.000   0.000;
    -0.939   0.000   0.000   0.000;
     0.000   0.000   0.000   1.000;

    Do you know why I get this error?
    MRIresample(): source matrix has zero determinant; matrix is:
    -0.000  -0.000  -0.000   0.000;
    -0.000  -0.939  -0.000   0.000;
    -0.939   0.000   0.000   0.000;
     0.000   0.000   0.000   1.000;

    Any help would be appreciated.

    John Drozd
    PostDoctorate Fellow

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