How to fix a nii or rec file with partial volume The problem I have is that the MRI scan is stopped manually, before the exam card is completed.
Thus data anaylsis programs read the header and expect a certain number of volumes but it has less, and on top of that the final volume is partial so I can't simply modify the header so that it looks for less.
Programs such as fslroi that allow trimming volumes do not handle partial volumes.
How can I remove the partial data so that the file is correctly read?
I found the solution using the python package nibabel.
The code is rather simple. If filename is your nii, or rec file use:

import nibabel as nib
img = nib.load(filename,permit_truncated=True)
print("Saving image with shape:",img.shape)
nib.save(img,"truncated_{0}".format(filename))