mri_convert SC dicom - Freesurfer

14 Nov 2006


      Hi folks,
I was trying to convert an dicom MPRAGE with a SISCOM activation( grayscale )
to nii format to use the activation for a seed for probalistic fiber tracking.
The siscom is created in Analyze(program not file format) and then
exported to dicom , so it is a secondary capture siscom.
I know this is not really a freesurfer thing but I guess you guys when possible try to make your tools mutually usefull so I send the error in case you see a simple fix by an option I can apply. set orientation seems to be the issue  notice k_ras = (nan, nan, nan) also WARNING: NumberOfFrames 0 != Found Count of slices 104.
thanks if you can help
Greg.
reading from i170927.SCPT.1...
104 DICOM 3.0 files in list
Found 104 DICOM Files
WARNING: NumberOfFrames 0 != Found Count of slices 104.
reading DICOM image...
-------------------------------------------------
DICOM meta-header
file name                       /home/gkirk/tillsis/dicom/i170927.SCPT.1
Date and time
        study date              20061114
        study time              142154
        series time             142014.000000
        acquisition time        142014.000000
Identification
        patient name            
        manufacturer            SIEMENS NM
Dimensions
        number of rows          256
        number of columns       256
        number of frames        104
        pixel width             1
        pixel height            1
        slice thickness         2
        field of view           256
        image number            1 (might be not reliable)
        transfer syntax UID     1.2.840.10008.1.2.1
Acquisition parameters
        echo time               4.7
        repetition time         1870
        inversion time          1100
        echo number             0
        flip angle              0.261799
        bits allocated          8
Spatial information
        first image position    -132.963 -132.808 -122.125
        last image position     -132.963 -132.808 -122.125
        image orientation       1 -2.05103e-10 0 2.05103e-10 1 0
-------------------------------------------------
TR=1870.00, TE=4.70, TI=1100.00, flip angle=15.00
i_ras = (-1, 2.05103e-10, 0)
j_ras = (-2.05103e-10, -1, 0)
k_ras = (nan, nan, nan)
Reslicing using trilinear interpolation
MRIresample(): source matrix has zero determinant; matrix is:
-1.000  -0.000   nan   nan;
 0.000  -1.000   nan   nan;
 0.000   0.000   nan   nan;
 0.000   0.000   0.000   1.000;
[gkirk@Nuit dicom]$