ImageJ does not use NIfTI scl_slope and scl_inter when loading

Open johnmarianhoffman opened this issue 3 years ago • 1 comments

I have a NIfTI1 file that's floating point data "compressed" into uint16s and uses these fields to recover the original floating point values. 3DSlicer does automatically rescale these values when loading, however when loading the same file in ImageJ, ImageJ only has the original uint16 data.

Sample file can be found here: https://drive.google.com/file/d/1gs-tvNvHznsHgjO2ACSRbtg-Z9kqZ2tH/view?usp=sharing

Totally fine if this is not supported and not intended for support, but it'd be helpful to know if I need to offer it as an option for the software I'm working on.

Sep 30 '22 16:09 johnmarianhoffman

I’m experiencing the same issue using ImageJ 1.54p with SCIFIO or Bio-Formats 8.0 plugin to read NIfTI data that was processed using my Python scripts. The result is the same

FIJI only displays the raw uint16 values and does not rescale the data based on the scl_slope and scl_inter values in the NIfTI header. It would be great if ImageJ had an option to automatically apply intensity scaling during import, or at least allow for manual adjustment of the scaling.

Ps. My environment is macOS 15.3.2 (AArch64) and Java 11.0.26

Mar 21 '25 19:03 cecilyen