When I use the following to3d command on oblique data from a Bruker 4t running Siemens Dicom:
to3d -epan -skip_outliers -assume_dicom_mosaic -prefix killme1b.raw -time:zt 32 140 2000 alt+z -@ < dimon.files.run.002
I get the following output:
++ to3d: AFNI version=AFNI_2007_05_29_1644 (Aug 27 2007) [32-bit]
++ Authored by: RW Cox
*+ WARNING: TR expressed in milliseconds will be converted to TR=2.000000s
++ Counting images: total=4480 2D slices
++ DICOM WARNING: file inhib1/_.MR._.2.1.2007.4.3.11.41.13.875000.7669115.IMA has Window tags; setenv AFNI_DICOM_WINDOW YES to enforce them
++ DICOM NOTICE: 6x6 Siemens Mosaic of 32 64x64 images in file inhib1/_.MR._.2.1.2007.4.3.11.41.13.875000.7669115.IMA
++ Data detected to be oblique
++ Each 2D slice is 64 X 64 pixels
++ Voxel dimensions: 3.5938 X 3.5938 X 3.8500 mm
++ Image data type = short
++ Reading images: ++ DICOM WARNING: file inhib1/_.MR._.2.33.2007.4.3.11.41.13.890000.7669130.IMA has Window tags; setenv AFNI_DICOM_WINDOW YES to enforce them
++ DICOM NOTICE: 6x6 Siemens Mosaic of 32 64x64 images in file inhib1/_.MR._.2.33.2007.4.3.11.41.13.890000.7669130.IMA
++ DICOM WARNING: no more Window tags messages will be printed
++ DICOM NOTICE: no more Siemens Mosaic messages will be printed
..........................................
*+ WARNING: Image Positions do not lie in same directionas cross product vector - 1.000000
*+ WARNING: Slice-based center is different from mosaic center
*+ WARNING: Origin computation of obliquity may be incorrect
Mosaic Center: 0 -8.12165 10.8193
Slice-based Center: -9999.9 -8.12169 10.8193
Mosaic Center: 0 -8.12165 10.8193
Origin Coordinates: -113.203 -134.586 -8.74921
++ Command line TR=2000ms ; Images TR=2s
++ 3D dataset written to disk
What I'm concerned about are the warning messages at the end, indicating a problem with the mosaic center and slice centres not aligning. I've not previously analysed data from this scanner, and never analysed oblique data (I've read the readme on oblique data, but it doesn't seem to explain this warning), so I'm not sure what is causing the error, what it necessarily means, and what I should do about it. Any help would be greatly appreciated.