Closed seokjin9804 closed 11 months ago
It looks like your args weren't parsed correctly because the command includes
--output [ output,outputWarped.nii.gz,outputInverseWarped.nii.gz ]
It did not get your option "-o brain1_tobrain2" for some reason. To debug further, please include all output. Run
antsRegistrationSyNQuick.sh -d 3 -f test_brain1.nii.gz -m test_brain2.nii.gz -o brain1_to_brain2_ 2>&1 | tee quick.txt
You can drag and drop the file quick.txt into the comment box
Thank you so much for replying. Today, I tried rigid and affine registration, and actually they generated output files. However when I tried deformable registration they killed the run like below image.
Here is the quick.txt
OK, it looks like you fixed the output naming. But the antsRegistration process is being killed by the system. It could be a memory or CPU time limitation on your system.
If you can share data I will run the same command on my machine just to verify it's not the data itself.
Was this issue solved? I'm facing a similar problem...
Was this issue solved? I'm facing a similar problem...
I'm not sure what the issue was. You're welcome to open a new issue, please fill out the template and include all terminal output from the commands you ran.
If you can make a runnable example (using your data or any public data) I will run it
Describe the problem
I'm using windows and following below tutorials. https://dataportal.brainminds.jp/ants-tutorial. I successfully compiled and installed ANTs and finally could run "antsRegistrationSyNQuick.sh -d 3 -f test_brain1.nii.gz -m test_brain2.nii.gz -o brain1_to_brain2_". However I could not find any output files in the directory. Below is the printed out result. Thanks. Registration finished. The antsRegistration call was: -------------------------------------------------------------------------------------- /opt/ANTs/bin//antsRegistration --verbose 1 --dimensionality 3 --float 0 --collapse-output-transforms 1 --output [ output,outputWarped.nii.gz,outputInverseWarped.nii.gz ] --interpolation Linear --use-histogram-matching 0 --winsorize-image-intensities [ 0.005,0.995 ] --initial-moving-transform [ test_brain1.nii.gz,test_brain2.nii.gz,1 ] --transform Rigid[ 0.1 ] --metric MI[ test_brain1.nii.gz,test_brain2.nii.gz,1,32,Regular,0.25 ] --convergence [ 1000x500x250x0,1e-6,10 ] --shrink-factors 12x8x4x2 --smoothing-sigmas 4x3x2x1vox --transform Affine[ 0.1 ] --metric MI[ test_brain1.nii.gz,test_brain2.nii.gz,1,32,Regular,0.25 ] --convergence [ 1000x500x250x0,1e-6,10 ] --shrink-factors 12x8x4x2 --smoothing-sigmas 4x3x2x1vox --transform SyN[ 0.1,3,0 ] --metric MI[ test_brain1.nii.gz,test_brain2.nii.gz,1,32] --convergence [ 100x100x70x50x0,1e-6,10 ] --shrink-factors 10x6x4x2x1 --smoothing-sigmas 5x3x2x1x0vox -------------------------------------------------------------------------------------- Moving image resampled into fixed space: outputWarped.nii.gz Fixed image resampled into moving space: outputInverseWarped.nii.gz -------------------------------------------------------------------------------------- ![image](https://github.com/ANTsX/ANTs/assets/140678281/0576b641-6893-4021-91bb-b4e0aa26a4f8) **To Reproduce**System information (please complete the following information)
Additional information