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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



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