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June 13, 2022 12:17PM
Hi Daniel,

Thank you for your input. I have a follow up question. I also watched your video online as a reference (https://cbmm.mit.edu/video/09-alignment-and-atlases-part-1-2).

Questions pertaining my use: I want to register the EPI data set to say it's 5th brik. I wasn't originally trying to register it to an anatomical set. Would the following code be appropriate?

align_epi_anat.py \
-anat $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig  \
-epi $AnimalID/$FolderID/${AnimalID}_${FolderID}+orig \
-rigid_equiv \
-anat_has_skull no \
-epi_strip None \
-epi_base 5

My first attempt with this code produced a registered set ($AnimalID/$FolderID/${AnimalID}_${FolderID}_al+orig) that was completely off. Any feedback or clarity to the source code to use would be 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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