AFNI Message Board

Dear AFNI users-

We are very pleased to announce that the new AFNI Message Board framework is up! Please join us at:

https://discuss.afni.nimh.nih.gov

Existing user accounts have been migrated, so returning users can login by requesting a password reset. New users can create accounts, as well, through a standard account creation process. Please note that these setup emails might initially go to spam folders (esp. for NIH users!), so please check those locations in the beginning.

The current Message Board discussion threads have been migrated to the new framework. The current Message Board will remain visible, but read-only, for a little while.

Sincerely, AFNI HQ

History of AFNI updates  

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April 27, 2005 04:37PM
Just outside the visible part of the brain are many low-intensity-but-not-zero voxels. These are caused by Fourier ringing and ghosting artifacts in the MRI acquisition and reconstruction process. Normally, you don't see these, since their intensity is maybe 10% of the brightness of the main part of the image.

However, you are dividing by the mean 'b'. Where the image has low-but-not-zero intensity, b is small and so division by b will scale things up relative to the inside of the brain. As a result, you see the weird artifacts being amplified to the same scale as the brain. And some of these b values may be tiny, so you may get some huge voxels outside the brain, after scaling.

Then, since your input image is shorts, AFNI will rescale the output to be shorts by default. This leads to a scaling artifact, since shorts only store 16 bits of value, but AFNI has to allow for the huge values scaled up by division by small b values. As a result, the normal sized values end up getting squashed to a low number of bits, and you see the quantization effect in your 'bad' time series.

The solution you have is a good one. However, if you don't want to suppress the small-but-nonzero voxels, you can get around the issue by using the '-datum float' option to 3dcalc. This will store the output dataset in float format instead of short format, and thus avoid the scaling/quantization artifact.

By the way, nice use of image attachments -- this is why we enabled them!

Subject Author Posted

3dCalc division problem

Alan Anticevic April 27, 2005 04:03PM

Re: 3dCalc division problem

Robert Cox April 27, 2005 04:37PM

Re: 3dCalc division problem

Alan Anticevic April 27, 2005 04:41PM