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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Anonymous User
November 14, 2012 09:47PM
Hello,

I tried aligning two oblique anatomical scans from the same subject taken over different sessions using align_epi_anat.py, but the alignment is horrendous. This is the first time I've encountered such bad alignment with a single subject (about 35 deg difference in obliquity). Any idea what I'm doing wrong? I added the "-deoblique" option to the command but it has no effect. Is there any way to deoblique the data through afni_proc.py? Command as I'm using it below:

align_epi_anat.py -dset1 ${dset1} -dset2 ${dset2} -dset1to2 -dset1_strip 3dSkullStrip -dset2_strip 3dSkullStrip -cost lpa -feature_size 0.5 -deoblique on -prep_off -giant_move

Thanks,
Stefan
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Subject Author Posted

Aligning two oblique anatomical scans

Anonymous User November 14, 2012 09:47PM

Re: Aligning two oblique anatomical scans

Daniel Glen November 15, 2012 08:49AM

Re: Aligning two oblique anatomical scans

Daniel Glen November 15, 2012 01:56PM

Re: Aligning two oblique anatomical scans

Anonymous User November 15, 2012 07:54PM

Re: Aligning two oblique anatomical scans

Anonymous User November 15, 2012 08:24PM

Re: Aligning two oblique anatomical scans

Daniel Glen November 19, 2012 04:32PM