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

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3dFoodie
December 17, 2014 12:22PM
Hi all,

I have collected functional runs and spin echo field maps in the same space with the same acquisition parameters, but when I reconstruct them using dcm2nii I see that the R-to-L extent is 104 voxels and the A-to-P extent is 96 voxels for the functional runs, while it is reversed (104 voxels R-to-L and 96 voxels A-to-P) for the spin echo field maps. The DICOM matrix field 0051,100B says 96*104s for the spin echo field maps and 96p*104 for the functional runs. However the field maps have width: 192 and height: 208 while for the functional data these are flipped.

To use these together I need them to be in the same space, so my question is, how do I reorient them appropriately? Is there a way to do this with dcm2nii or to3d or 3dresample once they've alreayd been reconstructed? Or can I crop the images (I'd rather not)? And for future acquisitions is there a way to prevent this?

Thank you!
Michael
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Subject Author Posted

Orientation Problem

3dFoodie December 17, 2014 12:22PM

Re: Orientation Problem

Daniel Glen December 17, 2014 05:47PM

Re: Orientation Problem

ptaylor December 18, 2014 05:03AM

Re: Orientation Problem

Daniel Glen December 18, 2014 10:22AM