I'm trying to convert ROI niftis I created to ppm to use in a script, and I have read the slicer can do this but I need some assistance. What I'm trying to get is an image like the one attached - a set of sagittal slices with the ROI overlaid. I can get something like this using command:
slicer 10_T1.nii.gz 10_motorROI.nii.gz -A 10 10_motor.ppm
But I want sagittal slices, not axial, and I don't know why it's creating one very slender, long image file
Thanks,
Emily

Originally posted by Emily Dennis:


Hi! First, sorry for my english. Second, i think that you try to create a image version ir your results, its ok?. If it is the situation, you can use a MRIcroGL. In this you can load a brain template and overlay your results. All must have a ".nii" extension. You can create a 3D image or ir you want a sagital slice.

Thanks Carlos! I will give that a try!