ntustison / antsregistrationwithmaskexample Goto Github PK

First of all, great thanks to your shell. I will put more than one star if it is possible :)

I have brain image (fixed image): T1, T2 and label1. I also have another brain image(moving image): T1,T2, and label2. The T1 and T2 in same subject have been alignedNow, I want to align two subject together and I found your shell. It is very help full and it worked. I have register T1 image in moving image to T1 image in fixed image and the output is

./OutputNoMask/ants0GenericAffine.mat
./ants1InverseWarp.nii.gz
./ants1Warp.nii.gz
./antsInverseWarped.nii.gz
./OutputNoMask/antsWarped.nii.gz 

Now, I want to register the T2 in moving image to T2 in fixed image and label2 in moving image to label1 in the fixed image using the above transformation. How should I do? Do I need to convert the label value (from 0 to 8) to float number likes (0:0.0-->0.2, 1:1.0-->1.2....) and perform registeration? Thanks so much

This is my current solution but the label did not align

affineTransformImage=/OutputNoMask/ants0GenericAffine.mat
warpImage=/OutputNoMask/ants1Warp.nii.gz
input_label=/brain/seg.nii.gz
ref_imgage=/brain/t1_fixed.nii.gz
outputDirectory=./OutputNoMask
mkdir -p $outputDirectory

antsApplyTransforms -d 3 -i ${input_label} \
  -o ${outputDirectory}/labelwarp.nii.gz \
  -t  ${affineTransformImage}\
  -r ${ref_imgage}