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

History of AFNI updates  

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June 10, 2022 01:44PM
Hi All,

Hoping to find help with strategies in registering a time series of abdomen images. Respiratory motion is a bit tricky since all organs don't move exactly uniformly. I'm mostly interested in registering just one organ. So willing to use a mask with the base image but wasn't sure how to do that in 3dAllineate. I tried '-source_mask' but it completely threw off the registration (much worse than without). Below is what I previously tried.

# 2D REGISTER
3dAllineate \
-overwrite \
-prefix $AnimalID/$FolderID/${AnimalID}_${FolderID}.Reg \
-base $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig[0] \
-warp shift_only \
-parfix 3 0 \
$AnimalID/$FolderID/${AnimalID}_${FolderID}+orig

Any help to improve the registration is greatly appreciated. Thank you!

Edwin
Subject Author Posted

Help with Registration of Abdominal images

ebaldelo June 10, 2022 01:44PM

Re: Help with Registration of Abdominal images

ebaldelo June 10, 2022 02:56PM

Re: Help with Registration of Abdominal images

Daniel Glen June 10, 2022 05:28PM

Re: Help with Registration of Abdominal images

ebaldelo June 10, 2022 06:05PM

Re: Help with Registration of Abdominal images

Daniel Glen June 10, 2022 07:36PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 12:17PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 02:35PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 05:33PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 06:24PM

Re: Help with Registration of Abdominal images

ebaldelo June 13, 2022 06:27PM

Re: Help with Registration of Abdominal images

Daniel Glen June 13, 2022 08:00PM

Re: Help with Registration of Abdominal images

Daniel Glen June 14, 2022 09:38PM

Re: Help with Registration of Abdominal images

ebaldelo June 15, 2022 09:38AM

Re: Help with Registration of Abdominal images

Daniel Glen June 15, 2022 12:46PM