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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Wenzhu
May 12, 2009 11:45AM
Hi Dear AFNI experts,

I am analyzing some fMRI data and MPRAGE anatomical images. I used "to3d" to read these images in. I have oblique warnings for both images. I am wondering if I can skip "3dWarp -deoblique *" step.

Here are the reasons that I want to skip:

1. 3dinfo shows that the oblique angles are the same for both fMRI data and anatomical images.
2. Both images are in the AC-PC orientation.
3. I ran align_epi_anat.py to align MPRAGE to fMRI data. The alignment looks good.

My concerns of not doing "-deoblique" is that:

We are going to do group analysis with this data, so we will need to transform it into Talairach space using the command @auto_tlrc. Can this still be done with the oblique dataset? Besides the group analysis, are there other analysis steps I should also be worried if I don't deoblique the data?

Thanks a lot!

Wenzhu
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Subject Author Posted

Is deoblique necessary?

Wenzhu May 12, 2009 11:45AM

Re: Is deoblique necessary?

Daniel Glen May 12, 2009 12:04PM

Re: Is deoblique necessary?

Wenzhu May 12, 2009 05:15PM

Re: Is deoblique necessary?

Daniel Glen May 12, 2009 06:48PM

Re: Is deoblique necessary?

Wenzhu May 13, 2009 11:06AM