Hello,
I've been trying to use mri_convert (freesurfer-Darwin-tiger-stable-pub-v3.0.3) to reconstruct images from our Siemens Magnetom Trio. When I type:
mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_ A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img
DB*.IMA and Block1.img are the input and output files respectively, I get the output detailed below (the salient error seems to be that mri_convert can't find a useful transformation matrix).
Can you tell me what I can do to correct this problem? Many thanks in advance,
Paige Scalf
mri_convert -it siemens_dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info.
INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = 0, Min=-1073775504, MinMin = 0 mojo:/Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 paige$ mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img mri_convert -it dicom -ot analyze4d DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Block1.img reading from DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA... Getting Series No Scanning Directory INFO: Found 111 files in /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1 INFO: Scanning for Series Number 3 INFO: found 107 files in series INFO: loading series header info.
INFO: sorting. RunNo = 2 INFO: (120 110 50), nframes = 107, ismosaic=1 ERROR: incorreclty formatted version string syngo MR B17 found in dicom tag 18,1020 (len = 3 != 6) Numaris Version: syngo MR B17 Maj = -1073770984, Min=22021328, MinMin = -1610546680 107 DICOM 3.0 files in list Found 107 DICOM Files WARNING: NumberOfFrames 0 != Found Count of slices 107. reading DICOM image... ------------------------------------------------- DICOM meta-header
file name /Volumes/dubois/A0A1inhibition/DB_A0A1_318/Block1/DB_A0A1_318.MR.BECK-PAIGE_A0A1_INHABITION.0003.0001.2010.03.18.16.34.50.500000.21615932.IMA Date and time study date 20100318 study time 160300.312000 series time 162802.453000 acquisition time 162802.453000 Identification patient name DB_A0A1_318 manufacturer SIEMENS Dimensions number of rows 880 number of columns 960 number of frames 107 pixel width 2.13333 pixel height 2.13333 slice thickness 2.1 field of view 1877.33 image number 1 (might be not reliable) transfer syntax UID 1.2.840.10008.1.2.1 Acquisition parameters echo time 25 repetition time 3000 inversion time not found echo number 1 flip angle 1.5708 bits allocated 16 Spatial information first image position -1027.46 -12.1727 952.833 last image position -1027.46 -12.1727 952.833 image orientation 1 0 0 0 -0.00174528 -0.999998 -------------------------------------------------
TR=3000.00, TE=25.00, TI=0.00, flip angle=90.00 i_ras = (-1, -0, 0) j_ras = (-0, 0.00174528, -0.999999) k_ras = (nan, nan, nan) Reslicing using trilinear interpolation MRIresample(): error inverting matrix; determinant is nan, matrix is: -2.133 -0.000 nan nan; -0.000 0.004 nan nan; 0.000 -2.133 nan nan; 0.000 0.000 0.000 1.000;