I noticed that the output images and even the 001.mgz in orig folder are re-sliced into 255 slices although my input was 160 slices. Is there any way I can get the output image with same number of slices? as I need to use the masks of some structure for further analysis. In other words, I have registered one image to the original MPRAGE I have used in freesurfer in order to get a cc mask and multiply it by the registered image and in this case I need the number of slices exactly the same. Any idea please?

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