HI Rick,
thanks a lot for your help. I have now run the following
dcm_to_nii_command = sprintf("Dimon -infile_prefix '%s/*.dcm' -ushort2float -use_obl_origin -gert_create_dataset -gert_write_as_nifti -gert_outdir %s -gert_to3d_prefix %s", input_directory_path, ...
output_filepath, ...
output_filename);
however, I can see from the command window that is not doing what I want..please see screenshot attached
Also, I get the some dark spots in random places, sometimes in the middle of the brain, sometimes just outside
Best,
Cecilia
