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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JW
February 07, 2021 05:20PM
Dear AFNI experts,

I used align_epi_anat.py to align anat and epi files before running the proc py using the below script.

align_epi_anat.py \
-epi2anat \
-anat "$subj"."$cond"_SurfVol.nii \
-epi epi."$subj"."$cond".slicemocoxy_afni.slomoco+orig \
-epi_base 0 \
-anat_has_skull yes \
-epi_strip 3dAutomask \
-giant_move \
-volreg off \
-overwrite

Pre-alignment (upper image) was not bad but I wanted to make it better so ran the script, but I found that epi image became completely off from anat after running the align_epi_anat (below image). Could you please let me know how can I fix this?

Best,
JW
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Attachments:
open | download - pre_alignment.jpg (63.1 KB)
open | download - post_alignment.jpg (80.2 KB)
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Subject Author Posted

anat_epi alignment Attachments

JW February 07, 2021 05:20PM

Re: anat_epi alignment

ptaylor February 08, 2021 12:37PM

Re: anat_epi alignment Attachments

JW February 08, 2021 04:04PM

Re: anat_epi alignment

Daniel Glen February 08, 2021 04:21PM

Re: anat_epi alignment Attachments

JW February 08, 2021 06:02PM

Re: anat_epi alignment Attachments

JW February 11, 2021 09:10PM

Re: anat_epi alignment

Daniel Glen February 12, 2021 12:19AM