I'm not sure what the problem is. You say that they match when you load the T1 
and the sc. If so, what is the problem?

On 11/27/2019 7:57 AM, zorothustra wrote:

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Hello Freesurfer Developers,

I'm trying to get superior colliculus' ROI mannually by freeview. I load 
"orig.mgz" as volumes and set the "orig.mgz" as the ROI's template then draw 
the ROI and save it as a label file. After that I use "mri_label2vol --label 
sc.label --temp T1.nii --reg register.dat --o sc.nii", "T1.nii" is my initial 
structure image, "register.dat" got from the code:" tkregister2 --mov T1.nii 
--s SUB --regheader --noedit --reg register.dat", and it worked, but the 
coordinate mismatch, much different from the SC's position in the T1 space( 
Load T1.nii as volume and SC.label as ROI in freeview, and they are matched).
Can anyone help me? Thank you!

1)FreeSurfer version: freesurfer-local-build-dev-20191104
2)platform: Ubuntu 18.04







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