mri_convert problems - Freesurfer

23 Mar 2006


      Hi, I'm a new Freesurfer user, currently working with Fjell and Walhovd in
Oslo.
When trying to convert some new scans with mri_convert there seems to be a
problem with the reconstruction, also the signal intensity is in the
300-500 range. See attached image. It does not return any errors.
Could someone please point me in the right direction here?
Thank you
Inge K Amlien
Running on:
Freesurfer centos4 x86_64 stable 3.0
Fedore Core4
Output from mri_convert:
mri_convert
/labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm
/labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz
reading from
/labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_002.dcm...
Getting Series No
INFO: Found 130 files in
/labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649
INFO: Scanning for Series Number 2
Scanning Directory
INFO: found 128 files in series
INFO: loading series header info.
INFO: slice direction constructed from image direction cosines.
INFO: sorting.
RunNo = 1
INFO: Handedness changed to left-handed.
INFO: (512 512 128), nframes = 1, ismosaic=0
FileName               
/labdata/lab-data/testinge/E0000002/1.3.12.2.1107.5.2.6.22226.30000005112107174770300000649/E0000002_2_716.dcm
Identification
        NumarisVer        syngo MR 2004A 4VA25A
        ScannerModel      Symphony
        PatientName       E0000002
Date and time
        StudyDate         20051121
        StudyTime         094537.984000
        SeriesTime        095542.281000
        AcqTime           094657.180012
Acquisition parameters
        PulseSeq          *tfl3d1
        Protocol          t1_3d_mpr_sag
        PhEncDir          ROW
        EchoNo            0
        FlipAngle         15
        EchoTime          3.19
        InversionTime     1100
        RepetitionTime    2730
        PhEncFOV          0
        ReadoutFOV        0
Image information
        RunNo             1
        SeriesNo          2
        ImageNo           128
        NImageRows        512
        NImageCols        512
        NFrames           1
        SliceArraylSize   0
        IsMosaic          0
        ImgPos            -91.5886 131.5105 125.9759
        VolRes              0.5000   0.5000   1.3300
        VolDim            512 512 128
        Vc                  0.0297  -0.9996   0.0000
        Vr                 -0.0000  -0.0000  -1.0000
        Vs                 -0.9996  -0.0297   0.0000
        VolCenter         -172.8739   1.0416  -2.0241
        TransferSyntaxUID 1.2.840.10008.1.2.1
INFO: no Siemens slice order reversal detected (good!).
TR=2730.00, TE=3.19, TI=1100.00, flip angle=15.00
i_ras = (0.0296663, -0.99956, 0)
j_ras = (-0, -0, -1)
k_ras = (-0.99956, -0.0296663, 0)
writing to /labdata/lab-data/testinge/testE0000002/mri/orig/001.mgz...
Scan info from nICE:
Manufacure's model name (0008,1090): Symphony
Scanning sequenece (0018,0020): IR\GR
Scanning variant (0018,0021): SP\MP
Scan options (0018,0022): IR
Acquisition type (0018,0023): 3D
Scan (Sequence) Name (0018,0024): *tfl3d1
Protocol Name (0018,1030): t1_3d_mpr_sag
Repetition time, TR (ms)(0018,0080): 2730.0
Echo time, TE (ms) (0018,0081):  3.2
Inversion time, TI (ms) (0018,0082): 1100.000
Flip angle (deg) (0018,1314): 15
Pixel spacing X (mm) (0028,0030):    0.5000
Pixel spacing Y (mm) (0028,0030):    0.5000
Slice thickness (mm) (0018,0050):    1.3300
Slice spacing or gap (mm) (0018,0088):   0.0000
FoV (freq*phase, mm):  256.0000 *  256.0000
Rect. FoV percentage: 100.0
No of PE steps (0018,0089): 192
Turbo Factor (ETL) (0018,0091): 1
Scan Percentage (0018,0093): 75.0
Pixel Bandwidth (Hz) (0018,0095): 190.0
Number of averages (0018,0083): 1
Recon resolution (Rows) (0028,0010): 512
Recon resolution (Columns) (0028,0011): 512
Image matrix size (X * Y pixels): 512 * 512
Scan number (0020,0012): 1
Image (instance) number (0020,0013): 128
Series number (0020,0011): 2