Hi,
I had a strange problem trying to convert DTI dicoms. When I used the following command to convert a raw dicom to nifti image, I obtained a 64-volume nifti that only contains one horizontal slice of the brain. mri_convert [input Dicom] [output nifti name]
Does anyone have ideas for why this might happen? Thanks.
Best, Jiahe
Here is the full log if it helps.
[cobham:dti] (nmr-stable53-env) mri_convert /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 dti_test.nii mri_convert /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 dti_test.nii $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940... Getting Series No Scanning Directory INFO: Found 3971 files in /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom INFO: Scanning for Series Number 53 INFO: found 64 files in series INFO: loading series header info.
INFO: sorting. RunNo = 52 INFO: (128 128 1), nframes = 64, ismosaic=0 PE Dir unknown UNKNOWN AutoAlign matrix detected AutoAlign Matrix --------------------- 0.998 0.043 0.047 -0.105; -0.045 0.998 0.053 -6.588; -0.045 -0.055 0.998 -24.537; 0.000 0.000 0.000 1.000;
This looks like an MGH DTI volume DTI is in non-moasic form, so cannot extract bvals/bvects FileName /autofs/cluster/iaslab/NMASA/mri/archive/nmasa_035_130430/dicom/MR.1.3.12.2.1107.5.2.32.35006.2013043010182341278836940 Identification NumarisVer syngo MR B17 ScannerModel TrioTim PatientName NMASA_035_130430 Date and time StudyDate 20130430 StudyTime 075408.863000 SeriesTime 101828.978000 AcqTime 100900.672500 Acquisition parameters PulseSeq unknown Protocol DIFFUSION_HighRes PhEncDir unknown EchoNo 1 FlipAngle 0 EchoTime 0 InversionTime -1 RepetitionTime 0 PhEncFOV 256 ReadoutFOV 256 Image information RunNo 52 SeriesNo 53 ImageNo 1 NImageRows 128 NImageCols 128 NFrames 64 SliceArraylSize 64 IsMosaic 0 ImgPos 0.0000 0.0000 0.0000 VolRes 0.0000 0.0000 0.0000 VolDim 128 128 1 Vc 0.0000 0.0000 0.0000 Vr 0.0000 0.0000 0.0000 Vs -0.0300 -0.6266 0.7788 VolCenter 0.0000 0.0000 0.0000 TransferSyntaxUID 1.2.840.10008.1.2.1 UseSliceScaleFactor 0 (slice 0: 1) INFO: no Siemens slice order reversal detected (good!). TR=0.00, TE=0.00, TI=-1.00, flip angle=0.00 i_ras = (0, 0, 0) j_ras = (0, 0, 0) k_ras = (-0.0299672, -0.626615, 0.778753) writing to dti_test.nii... WARNING: bad orientation matrix (determinant = 0) in nifti1 file ... ... continuing.