Hello,
I am using mri_convert to convert dicom image into analyze format using:
mri_convert -i PATH_TO_DICOM_HERE --out_type analyze -o analyze.img
The problem is:
The hdr.hist.orient in the output file is set to 0, but the pixels in the analyze image are saggital.
Does anybody have any suggestions as to what could be wrong?
Regards Mohana Ramaratnam
DIAGNOSTICS:
mri_info on the dicom reports:
Orientation : PIL Primary Slice Direction: sagittal
and that on the analyze image reports:
Orientation : LAS Primary Slice Direction: axial
OUTPUT of mri_convert:
INFO: Scanning for Series Number 4 INFO: found 176 files in series INFO: loading series header info.
INFO: sorting. RunNo = 3 INFO: (256 256 176), nframes = 1, ismosaic=0 PE Dir ROW ROW AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 0.038 -0.051 -2.542; -0.051 0.954 -0.294 -15.875; 0.038 0.296 0.954 -2.910; 0.000 0.000 0.000 1.000;
FileName FILE_NAME_HERE
Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName 65433 Date and time StudyDate 20110708 StudyTime 110252.125000 SeriesTime 111446.078000 AcqTime 110635.592500 Acquisition parameters PulseSeq tfl3d1_ns Protocol t1_mpr_1mm_p2_pos50 PhEncDir ROW EchoNo 1 FlipAngle 8 EchoTime 3.16 InversionTime 1000 RepetitionTime 2400 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 3 SeriesNo 4 ImageNo 1 NImageRows 256 NImageCols 256 NFrames 1 SliceArraylSize 1 IsMosaic 0 ImgPos 104.6950 154.3827 112.3121 VolRes 1.0000 1.0000 1.0000 VolDim 256 256 176 Vc -0.0493 -0.9976 0.0480 Vr -0.0403 -0.0460 -0.9981 Vs -0.9980 0.0511 0.0379 VolCenter 5.4129 25.2910 -5.9690 TransferSyntaxUID 1.2.840.10008.1.2.1 INFO: no Siemens slice order reversal detected (good!). TR=2400.00, TE=3.16, TI=1000.00, flip angle=8.00 i_ras = (-0.0492738, -0.997631, 0.0480037) j_ras = (-0.0402601, -0.0460391, -0.998128) k_ras = (-0.997974, 0.0511142, 0.0378956) writing to 110708_TC33875.img... Analyze Output Matrix -0.049 -0.040 -0.998 105.782; -0.998 -0.046 0.051 155.375; 0.048 -0.998 0.038 113.224; 0.000 0.000 0.000 1.000; -------------------- No such orientation specified in Analyze7.5. Set orient to 0 Direction cosines for FILE_NAME_HERE are: x_r = -0.0493, y_r = -0.0403, z_r = -0.9980, c_r = 5.4129 x_a = -0.9976, y_a = -0.0460, z_a = 0.0511, c_a = 25.2910 x_s = 0.0480, y_s = -0.9981, z_s = 0.0379, c_s = -5.9690 INFO: set hdr.hist.orient to 'transverse unflipped'