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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Janani
February 14, 2008 02:22AM
I have been attempting to align an anatomical image to an epi timeseries data set. I have been using 3dAllineate and 3dAnatNudge and been facing problems with both. All of my data are oblique.

3dAllineate - image size is reduced and in all views, the bottom part is slightly cut off

3dAllineate -base epi+orig \
-input anat+orig \
-prefix anat_aln+orig \
-mi \
-warp shift_only

3dAnatNudge - using 3dIntracranial causes large parts of brain structures to be removed leaving only small brain volumes (this occurred for some but not all anatomical data sets). For those datasets that did align, the sagittal view is shifted upwards and to the right.

3dbucket -fbuc -prefix fb+orig epi+orig
3dIntracranial -anat anat+orig -prefix anat+spgr_st+orig
3dAnatNudge -anat anat+spgr_st+orig \
-epi fb+orig \
-prefix anat_nudge+orig


Where am I going wrong? And, which command is better to use for my purposes? I appreciate the help!

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Subject Author Posted

3dAllineate vs. 3dAnatNudge

Janani February 14, 2008 02:22AM

Re: 3dAllineate vs. 3dAnatNudge

Ziad February 14, 2008 05:10PM

Re: 3dAllineate vs. 3dAnatNudge

Janani February 21, 2008 10:11AM