AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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September 06, 2007 01:09AM
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.

Subject Author Posted

mosaic warning message

Rob Hester September 06, 2007 01:09AM

Re: mosaic warning message

Daniel Glen September 06, 2007 08:53AM

Re: mosaic warning message

rick reynolds September 06, 2007 09:04AM