imagej / imagej/ImageJ

ImageJ does not use NIfTI scl_slope and scl_inter when loading

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#178 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
Java
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Description

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.

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Research direction

Start by reproducing the report with the linked sample NIfTI1 file and inspect ImageJ's NIfTI loading path. Determine whether loading should apply scl_slope and scl_inter to recover the floating-point values; done should be a confirmed behavior change or a clear decision that this is unsupported.

Written by the indexing model from the issue text.

Assessment

Tech stack
java
Domain
computer-vision
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Needs clarification
Newbie friendliness
35/100

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