Comments (7)
I expect it's because of antsAI downsampling the images too much. I can work on a fix, but in the interim, you could try getting an initial transform with
antsRegistrationSyNQuick.sh -f vic_ants/vic_NMT_prior.nii.gz -m vic_ants/vic_N4.nii.gz -t r -o vicToNMT_Affine
and then adding
-r vicToNMT_Affine0GenericAffine.mat
to the antsBrainExtraction.sh
command.
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Initial affine worked for me, BTW
![image](https://private-user-images.githubusercontent.com/611507/291651304-5b2ae39e-f797-48a6-a10c-f586d79c69d4.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.eyJpc3MiOiJnaXRodWIuY29tIiwiYXVkIjoicmF3LmdpdGh1YnVzZXJjb250ZW50LmNvbSIsImtleSI6ImtleTUiLCJleHAiOjE3MDk2NDU3MDgsIm5iZiI6MTcwOTY0NTQwOCwicGF0aCI6Ii82MTE1MDcvMjkxNjUxMzA0LTViMmFlMzllLWY3OTctNDhhNi1hMTBjLWY1ODZkNzljNjlkNC5wbmc_WC1BbXotQWxnb3JpdGhtPUFXUzQtSE1BQy1TSEEyNTYmWC1BbXotQ3JlZGVudGlhbD1BS0lBVkNPRFlMU0E1M1BRSzRaQSUyRjIwMjQwMzA1JTJGdXMtZWFzdC0xJTJGczMlMkZhd3M0X3JlcXVlc3QmWC1BbXotRGF0ZT0yMDI0MDMwNVQxMzMwMDhaJlgtQW16LUV4cGlyZXM9MzAwJlgtQW16LVNpZ25hdHVyZT1kMTJiZjBiZGQ3YjZhOGIxYzhkMDNkNzM2ZWUwNDQxZDIwMDIwNGIxM2I2NTUyMjEyZTFlZmFmN2NiNmU4ODUyJlgtQW16LVNpZ25lZEhlYWRlcnM9aG9zdCZhY3Rvcl9pZD0wJmtleV9pZD0wJnJlcG9faWQ9MCJ9.55_uuStZB-I27P_TRLe6dWK0tA9ZLAl6-H6I02XXa7U)
from ants.
Can you upload the full input dataset so that we can reproduce the issue on our end?
from ants.
Can you upload the full input dataset so that we can reproduce the issue on our end?
Thanks a bunch for your help. Unfortunately, the file size was too large to upload directly to GitHub,so I've uploaded the files to Google Drive. You can download them using the following link:
https://drive.google.com/drive/folders/1yf8d0uEasbpz0alxk70H-SM4pMIMQmqa?usp=sharing
Here's the command I used (note:name=vic):
$ANTSPATH/antsBrainExtraction.sh -d 3 -a ${name}_N4.nii.gz -e ${name}_NMT_prior.nii.gz -m ${name}_NMT_brainmask_prob_prior.nii.gz -o ${name}_ -f ${name}_NMT_brainmask_prior.nii.gz
Additionally, my goal is to perform segmentation and utilize the results to generate surfaces in FreeSurfer, following the workflow outlined below:
https://prime-re.github.io/structural/surfaces_and_flatmaps_notebook/Surfaces_and_Flatmaps.html
Thank you for your time and assistance.
from ants.
Thanks for your effective help! It works well :D
from ants.
I expect it's because of antsAI downsampling the images too much. I can work on a fix, but in the interim, you could try getting an initial transform with
antsRegistrationSyNQuick.sh -f vic_ants/vic_NMT_prior.nii.gz -m vic_ants/vic_N4.nii.gz -t r -o vicToNMT_Affine
and then adding
-r vicToNMT_Affine0GenericAffine.mat
to the
antsBrainExtraction.sh
command.
Dear cookpa
I have met the same problem when using antsBrainExtraction.sh and antsCorticalThickness.sh to deal with monkey brains. I tried your solution and It works when using antsBrainExtraction.sh. But I didn't find the same argument (antsBrainExtraction.sh -r to do the Initial moving transform) in antsCorticalThickness.sh.
Since antsCorticalThickness.sh calls antsBrainExtraction.sh , I am wondering whether the same argument to do the Initial moving transform should be added to _antsCorticalThickness.sh pipeline as well?
Besides, when I am doing antsRegistrationSyNQuick.sh to get an initial transform, if I have to add the "-t r" argument to specifiy the "rigid" transform type? Since some T1 imgs can't be well registered only by using rigid transform.
from ants.
The -t r
is just to do a fast initial transform. It's only a starting point for the rest of the registration, so it's OK if it's not a very good alignment. You can switch to -t a
if you like.
Regarding antsCorticalThickness.sh
, it doesn't support an initial transform but it will find an existing brain mask. So if you run it with -o myOutput_
and there exists myOutput_BrainExtractionMask.nii.gz
, it will not re-run the brain extraction and will carry on from the next step.
from ants.
Related Issues (20)
- Poor non-linear registration (SyN) for intra-participant T1 to fMRI EPI HOT 1
- Warnings possibly indicating problems HOT 3
- Clean up fully merged branches HOT 3
- Determining optimal hyperparameter settings for abdominal CT image registration HOT 6
- Warnings are raised when ANTs is used via CMake FetchContent HOT 4
- error in TensorFunctions.h during make on macOS with M2 chip HOT 8
- Spatial resolution and antsApplyTransforms HOT 2
- Atropos with `-k ManifoldParzenWindows` results in a segmentation fault HOT 8
- ANTs Version: 2.5.1.post1-g128c124 still requires ANTSPATH HOT 5
- Confusion over mi vs mi2 metric HOT 2
- Unexpected antsRegistrationSynQuick Result HOT 1
- "ITK ERROR: ITK only supports orthonormal direction cosines" when using antsRegistrationSyN.sh HOT 11
- web interface / gui for ANTs? HOT 10
- Are Jacobean values log transformed by default in CreateJacobianDeterminantImage command? HOT 2
- Port antsRegistrationSyN.sh to Windows HOT 2
- antsApplyTransforms not able to read transform txt HOT 7
- deformation field units HOT 1
- ImageMath TimeSeriesDisassemble 'std::out_of_range' HOT 2
- ImageMath TimeSeriesAssemble HOT 9
- Warping MNI Atlas to Native Space Through Single Subject Template HOT 4
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