I converted a set of FDG dynamic  images from Siemens MR PET to nifti but the values are much too high.  Using our in house software the image values on the same structure are more than 3 times lower and in the range that I would expect. 
Any help would be greatly appreciated.
Jean

Can you check that you are using the latest release of dcm2niix
  https://github.com/rordenlab/dcm2niix/releases
If that does not work, I suggest you press the "Issue" button on dcm2niix's github page and create a new issue. Also, you may want to make sure that the software you are using to measure these values uses the NIfTI scl_slope and scl_inter values. The raw data in the NIfTI image is the same as in the DICOM image, and the scl_slope and scl_inter come from the DICOM header (rescale intercept (0028,1052), rescale slope (0028,1053)).

Jean-

Thanks for confirming that your software was ignoring the scale slope and intercept factors. For others who have similar issues, dcm2niix is a lossless converter.So if  the raw DICOM data is stored as 16-bit integers, the NIfTI data will be stored as 16-bit integers. The DICOM header values rescale intercept (0028,1052) and rescale slope (0028,1053) will be saved as the NIfTI header values scl_inter and scl_slope. Software that reads the image should apply these scaling factors to the image data (unless the image data is 64 bit float). 

If you have software that ignores these values, you can apply them by using
 fslmaths in.nii.gz -add 0.0 out.nii.gz
Since the default output format of fslmaths is 32-bit float, it will apply the scale factors to the image data. However, the resulting images will require more disk space and be slower to read and save. The influence of this conversion would look like this:


fslhd in.nii.gz
...
data_type INT16
...
scl_slope 1.000000
scl_inter -1024.000000
fslhd out.nii.gz
...
data_type FLOAT32
...
scl_slope 1.000000
scl_inter 0.000000