CAT12 - badTissueContrast - beginner tutorial


I am new to CAT12 and heard lots of good things about it. I am following the instructions detailed in the CAT12-manual.pdf but I am getting the following error:


Bad tissue contrast (BG=0.16, CSF=59.02, GM=746.55, WM=13.26): This can be the result of (i) an improper SPM segmentation caused by failed affine registration, (ii) improper image properties with low contrast-to-noise ratio, or (iii) by preprocessing error. Please check image orientation and quality.

I checked the orientation as suggested in the tutorial, but it looks right?

Can anyone please give me pointers on how to overcome this bug.

To summarize I just opened CAT12 and selected "Segment". I selected the nifti file and clicked on the green arrow in the batch editor.

Thanks again,

This is a question for the CAT12 developers.
@CGaser ?

Hi @emdim,

the newest CAT12 version r1738/r1739 should solve some of the issues that occurred in the past with bad tissue contrasts. If not, I wonder whether you really have a T1-weighted image or any other modality which might not work with CAT12.



1 Like

Thank you @CGaser. I will see what version I do have.
Concerning the T1, I believe it is a T1 from the Uk biobank.

Thanks for the fast answer.
Also, if here is not the right place to ask, please let me know and I apologize.