Thanks! I tried it out and it works great.
A couple more related questions:
1) in order to use -roi it appears the voxel coord (not the mm coord) must be used. Is there any easy way to convert from mm to voxel without going into fslview? I found one of your previous post where it says to use
std2imgcoord -img image_name -vox coord_file
however, It doesn't appear to work for me. I am putting the anatomical image in for -im and then the coord file with xyz on one line seperated by spaces.
2) instead of writing fslmaths -roi 70 times is there a way to input a file with all of the relevant coordinates and have it create the roi's with different names?
Thanks again for your help
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