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:
[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
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Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
