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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Karelo
February 25, 2020 12:40PM
Dear AFNI team,

I am doing registration between EPI images and its T1. The registration is almost perfect in all subject except in one (73 of 74 subjects). I would like to attach the code that I am using to perform the registration. 

align_epi_anat.py  -anat  T1 \
-epi  EPI \
-epi_base BASE_VOLUME  \
-epi2anat   \
-suffix _pre.nii  \
-anat_has_skull no \
 -epi_strip 3dAutomask  \
-volreg off -tshift off -deoblique off  \
-master_epi  T1 \
-cost lpc

I put tshift and volreg in 'off' because I already did those step in a preprocessing pipeline.
What could be a possible cause for a bad registration? I would also like to attach a jpeg of the subject who has the registration problem.

Thanks in advance,
Karel
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Attachments:
open | download - registration.jpg (3.9 KB)
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Subject Author Posted

Problem in registration in a particular subject Attachments

Karelo February 25, 2020 12:40PM

Re: Problem in registration in a particular subject

Daniel Glen February 25, 2020 12:49PM

Re: Problem in registration in a particular subject

Karelo March 03, 2020 10:15AM