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.
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.