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: > > [jdr...@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: > > [jdr...@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: > > [jdr...@trumpet orig]$ cp T1.mgz ../rawavg.mgz > [jdr...@trumpet orig]$ cd .. > [jdr...@trumpet mri]$ ls > 1.Bvq.Xml* 2.Bvq.Xml* error.log orig/ orig2/ rawavg.mgz > transforms/ > [jdr...@trumpet mri]$ pwd > > /trumpet/downloads/FreeSurfer/freesurfer/subjects/buckner_data/tutorial_subjs/convertedfile/mri > > Then I tried to conform the data using: > > [jdr...@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 > > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
