So I used MCFLIRT and it worked, but some voxel intensities changes in a strange way. I attach an image with the original nifti on the left and the mcflirted one on the right. I used the center volume of the same image as a reference, so I didn't expect any change:
mcflirt -in filtered_func_data.nii.gz -reffile center_vol -out filtered_func_data_reg
Do you know how can this be fixed?
Thanks again!
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