to3d dicom conversion signed 16-bit format failure

Hello all,

I’m using to3d to convert my dicoms collected using a CMRR-sequence MB2 sequence. It seems that to3d writes data out in signed 16-bit format, this causes very high values (>32000?) to be written out as negative values. See black spots visual cortex attached image.

I’m using the following command
to3d -prefix run_1 -time:zt 42 151 2000 FROM_IMAGE *.dcm

How can the dicoms be converted in AFNI to a different format (e.g. 32-bit)?


Hi Jasper,

Try adding the option -ushort2float. Note that AFNI does
need such a conversion, because it does not support
unsigned shorts.

  • rick

Many thanks Rick, this solved the problem!