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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naailk90
August 08, 2019 09:58AM
Hello everyone,

I am trying to align my anatomical to my functional however I am getting very poor results for some participants (see attached images). After alignment the anatomical looks very wonky and this was happening on quite a few participants. I have tried using different cost functions such as lpa and nmi but have had no luck. When I try the alignment on another computer with an older version of afni the alignment looks good.

Computer 1 (mis-aligned): Afni version: 19.2, AMD chipset, Ubuntu 18.04
Computer 2 (well-aligned): Afni version 18.3, Intel Chipset, MacOS High Sierra

Here is the command I was using:

align_epi_anat.py -overwrite -anat2epi -anat MPRAGE1.nii \
-suffix test_al \
-epi vr_base_min_outlier+orig -epi_base 0 \
-epi_strip 3dAutomask \
-cost lpc+ZZ \
-volreg off -tshift off

Thanks for any help,

Naail Khan
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Attachments:
open | download - Screenshot from 2019-08-08 09-55-21.png (207.8 KB)
open | download - Screenshot from 2019-08-08 09-53-27.png (217 KB)
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Subject Author Posted

Significantly mis-aligned data from align_anat_epi.py Attachments

naailk90 August 08, 2019 09:58AM

Re: Significantly mis-aligned data from align_anat_epi.py

Daniel Glen August 08, 2019 05:51PM