The research by a team of German researchers involved data from 30 brain scans fed into the computer using a package called FreeSurfer.
The software is one of the major medical image analysis programmes used across the globe to measure the size of different parts of the brain.
The researchers found that not only did Windows and Mac OS installs of the software produce different results - but the version of Mac OS also showed variation, according to Gizmodo.
The findings by a team of German researchers has now raised concerns about the way crucial scans such as CT and MRI are analysed in routine practice.
Each time the software was used it measured the size and thickness of various structures of the brain and the level of differences between computers varied depending on brain location.
For Mac vs PS and Mac OS updates the difference was closer to 2-5 per cent, but there was a 15 per cent variation just because of a Mac OS update.
The reason behind the discrepancies in the results, however remains unclear.
"The main conclusion is that in the context of an ongoing study, users are discouraged to update to a new major release of either FreeSurfer or operating system or to switch to a different type of workstation without repeating the analysis; results thus give a quantitative support to successive recommendations stated by FreeSurfer developers over the years," US National Library of Medicine National Institutes of Health abstract concludes.