Hi Jeremy,

That seems strange, I looked in more detail at the error stack and the "permission denied" error seems to come up when attempting to open the file C:\Users\cnl1796\Documents\Jeremy\tDCS_Patient_Study\Data\mri\Data\tDCS_TBI_01_01_A\SCANS\3\nii\cmrr_mb4_restingstateTE28.nii with r+ permissions (for reading and writing) as part of the realignment step, could you please copy/paste the following in Matlab command line:
filename='C:\Users\cnl1796\Documents\Jeremy\tDCS_Patient_Study\Data\mri\Data\tDCS_TBI_01_01_A\SCANS\3\nii\cmrr_mb4_restingstateTE28.nii';
a=spm_vol(filename);
disp(a);
disp(a(1).private.dat);
fh=fopen(filename,'r+');
disp(fh);
fclose(fh);