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
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
Hi Doug,
What about the translations? I haven't found anything like -iid in mri_convert for the translation parameters. Can I take the -im MATRIX option? Assuming the Matrix contains the cosines in the first three columns and in the last the coordinates of the voxel in the corner, like the in the dicom header.
Joerg
Doug Greve schrieb:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Use the --in_center option to spec the center of the volume.
Joerg Magerkurth wrote:
Hi Doug,
What about the translations? I haven't found anything like -iid in mri_convert for the translation parameters. Can I take the -im MATRIX option? Assuming the Matrix contains the cosines in the first three columns and in the last the coordinates of the voxel in the corner, like the in the dicom header.
Joerg
Doug Greve schrieb:
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
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Jörg Magerkurth Diplom-Physiker Klinikum der Johann Wolfgang Goethe Universität Institut für Neuroradiologie Schleusenweg 2-16 (Haus 95) 60528 Frankfurt Tel: (++49)(+69)6301-83822 Fax: (++49)(+69)6301-7176 www.bic.uni-frankfurt.de
freesurfer@nmr.mgh.harvard.edu
-
Doug Greve -
Joerg Magerkurth