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Optimizing EPI to T1 MPRAGE registration #1734
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Hi, (Note the script and example data have brain.nii and brainmask.nii mixed up naming wise, I have preserved this in my example) Here's my crack at optimizing the registration, changes made
Note that at the end of this, the intention is to align JUST the brainstem, if I were doing a full registration where I want to explicitly also focus on the brainstem, I would do a SyN without the masks, and then refine the SyN in the masked area again. This hard-coded script is based on the outputs from my generalized registration script antsRegistratioN_affine_SyN.sh from https://github.com/cobralab/minc-toolkit-extras/ P.S. The MPRAGE is a bit over-padded which will causes excess unneeded calculations that need to be done, cropping the FOV to be tighter would speed up the script.
Couldn't attach the file here, too large, but here's the ants_output files (resampled image, affine file, forward/reverse warp fields) |
Metadata says the file is post-Freesurfer, so its had lots of manipulation done to it |
Operating system and version
CentOS Linux 7 (Core)
CPU architecture
Unknown
ANTs code version
ANTs Version: 2.1.0.post764-g8bed0
ANTs installation type
Compiled from source
Summary of the problem
Hi,
I have a partial FOV EPI dataset that I am trying to register to the T1 MPRAGE with the goal of optimizing the registration in the brainstem, particularly at the boundary between the 4th ventricle and posterior brainstem. The partial FOV EPI has distortion in the A-->P direction, with some anterior in the anterior part of the brainstem, thus I have been using SyN to try and best register these two together. My approach that I will describe below has worked for most subjects so far, but I have a few subjects where despite many iterations of antsSyN the final registration is still several millimeters off (i.e. the registered functional has the 4th ventricle several slices anterior to the anatomical image). I have tried a few of the different trouble shooting suggestions I've seen in other GitHub issues, but none of have worked yet. I would like to first get a sanity check that I am not doing anything obviously wrong in my code, as well as the way I am trying to optimize over the brainstem. Second, if anyone has suggestions on how to go about iterating through the different registration steps I do to optimize the brainstem registration that would be helpful. I am somewhat new to ANTs so I don't have the best understanding about all of the parameters.
To optimize over the brainstem, I have been manually drawing binary masks in both anatomical and functional spaces covering the 4th ventricle and much of the brainstem. After Rigid and Similarity steps using just the brain masks to get the EPI somewhat aligned to the MPRAGE, I then use these brainstem masks in the affine and SyN steps of my antsRegistration call to optimize over the brainstem. Again, this has worked for many subjects with the attached script, but just a few I am having a hard time fixing.
Attached is:
I'm happy to provide any other information that would be helpful.
Thanks,
Nick
Commands to reproduce the problem.
example_ants_script.sh.zip
Output of the command with verbose output.
ants_script_output.txt
Data to reproduce the problem
ants_example.zip
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