To save some disk space, the anat and func/EPI datasets are stored only as .hdr files, keeping the headers without any actual data. The images were separated and deleted as in: cd sub-10506/anat nifti_tool -copy_image -infiles sub-10506_T1w.nii.gz -prefix t.hdr rm t.img sub-10506_T1w.nii.gz mv t.hdr sub-10506_T1w.hdr