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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Kyung
March 28, 2003 03:15PM
Hello,

I have a question about the to3d command for processing oblique slices.

We are currently doing fMRI experiments using a Siemens 3T Allegra and
we acquire an MRA, a 3D SPGR for high resolution anatomy and EPI for
functional scans. When we run EPI and 3D SPGR, we always copy parameters
from the MRA to scan the same slices. To3d works fine for this. But now,
when we do oblique slices, the to3d command does not work correctly. The
coordinates given in the 3dinfo output (I-S, A-P, R-L) do not match
between MRA, EPI, and 3D SPGR even though we copied the parameters from
MRA to the other scans. This causes a problem in overlaying EPI images
onto MRA and 3D SPGR images. We can correct this using 3drefit, but we
wonder if there is any known problem to processing DICOM images with
oblique slices using to3d. Please let us know if we are doing something
wrong.

Thanks for your help in advance.

Kyung

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Subject Author Posted

to3d for oblique scan

Kyung March 28, 2003 03:15PM

Re: to3d for oblique scan

bob cox March 29, 2003 08:45PM

Re: to3d for oblique scan

Kyung March 31, 2003 12:13PM