open-discussion > separate bilateral ROIs into left and right
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Jun 2, 2017 02:06 PM | J Han
separate bilateral ROIs into left and right
Dear everyone,
I'm trying to import FSL DTI thalamus subdivision seeds.
The problem is that these seeds are bilateral, but I want to separate them into right and left.
I can't find how to in manual.
Please let me know if someone knows how to.
Thanks a lot.
Jaewook
I'm trying to import FSL DTI thalamus subdivision seeds.
The problem is that these seeds are bilateral, but I want to separate them into right and left.
I can't find how to in manual.
Please let me know if someone knows how to.
Thanks a lot.
Jaewook
Jun 2, 2017 03:06 PM | yacila - University of Geneva
RE: separate bilateral ROIs into left and right
Hi Jaewook,
You divide the voxels that you got in the x direction (see the info in fslinfo) by two. Then use roi to tell the command that should cover all the direction (x,y,z)
Let's see you have 64 voxels, then your command should do both, extract the left side and binarize it:
fslmaths thalamus.nii.gz -bin -roi 32 -1 -1 -1 -1 -1 -1 -1 left_thalamus.nii.gz
for the right thalamus, you should only substract the left side from the bilateral mask...and also binarize in the same command.
I hope it hellps
Yacila
You divide the voxels that you got in the x direction (see the info in fslinfo) by two. Then use roi to tell the command that should cover all the direction (x,y,z)
Let's see you have 64 voxels, then your command should do both, extract the left side and binarize it:
fslmaths thalamus.nii.gz -bin -roi 32 -1 -1 -1 -1 -1 -1 -1 left_thalamus.nii.gz
for the right thalamus, you should only substract the left side from the bilateral mask...and also binarize in the same command.
I hope it hellps
Yacila