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  

Previous Message Next Message
Message List New Topic Print View
|
Brad Buchsbaum
February 15, 2008 06:51PM


Hi,

We're trying to examine a contrast image that was generated in SPM overlaid on an anatomical MRI. Both images are in NIFTI format. Both images have non-cardinal oblique transforms encoded in qforms (with sform = qform). The images have been coregistered in SPM5. In the SPM viewer, the images are well registered.

In the AFNI viewer, however, the images are clearly misaligned. So here is the question:

1. What does the AFNI viewer do with the qform? ignore it?

2. How do I get AFNI to use the qform information?

3. When I convert to AFNI format using 3dcopy, I see that the qform info shows up in the field "IJK_TO_DICOM_REAL" -- how is this information used?

4. clicking the button "warp underlay on demand" does not seem to get AFNI to use the qform info. Should it?


thanks,

Brad Buchsbaum
Reply Quote
RSS
Subject Author Posted

sform, obliquity, IJK_TO_DICOM_REAL

Brad Buchsbaum February 15, 2008 06:51PM

Re: sform, obliquity, IJK_TO_DICOM_REAL

rick reynolds February 15, 2008 09:40PM