You can give mri_convert input direction cosines for the cols, rows,
and slices (-iid, -ijd, -ikd), then load the volume into tkmedit to
see if you got it right. Note: this is a difficult and frustrating
process.
doug
On Sat, 16 Feb 2008, Joerg Magerkurth wrote:
Hi,
I have siemens mrs data which are exportet as raw data at the scanner.
I haven't still a possibility to convert it to dicom. But the header
entries looks similar to dicom. It contains Size entries and normal
vectors:
################
SliceThickness: 25.000000
PositionVector[0]: -140.282130
PositionVector[1]: -190.229627
PositionVector[2]: -149.289767
RowVector[0]: 0.990890
RowVector[1]: 0.030539
RowVector[2]: 0.131169
ColumnVector[0]: -0.017296
ColumnVector[1]: 0.994742
ColumnVector[2]: -0.100938
VOIPositionSag: -7.599275
VOIPositionCor: -26.662493
VOIPositionTra: -46.134291
VOIThickness: 80.000000
VOIPhaseFOV: 300.000000
VOIReadoutVOV: 300.000000
VOINormalSag: -0.133562
VOINormalCor: 0.097749
VOINormalTra: 0.986208
VOIRotationInPlane: -0.017453
FoVHeight: 300.000000
FoVWidth: 300.000000
FoV3D: 200.000000
PercentOfRectFoV: 1.000000
NumberOfRows: 16
NumberOfColumns: 16
NumberOf3DParts: 8
PixelSpacingRow: 18.750000
PixelSpacingCol: 18.750000
PixelSpacing3D: 25.000000
###########################
I want register other modalities to this file. So I need the fsl
registration matrix. I think there are several ways to do this:
- calculate manualy the qform and put it in a fake-nifi to do a
registration with tkregister over the header info
- make a fake dicom with the entries form the rda, try the same
My question:
Is there a better more direct solution without a fake file? Like giving
tkregister or a other tool the cosines and other information from the
header of the raw data and a second nifti file to obtain the fsl
registration matrix?
Best regards,
Jörg
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