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

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Colm Connolly
June 02, 2006 12:37PM
Hi all,

I created some brik files which represent % area under the curve %(auc) calculations from functional data which was not masked. When I load up the brik I get a bik gaping hole where the brain should be. The only data visible is the noise outside the brain. This says to me that the %auc briks need to be clipped. The problem is how do I decide on appropriate values to to pass to 3dmerge -2clip?

Why did I not use a brain mask in the first place? I'd like to pass the %auc files through fsl's flirt to do the normalisation and it seems to work best on data which hasn't been masked. I guess the key here is to avoid being over aggressive on the clipping.

Advice greatly appreciated.

Regards,

Colm.
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Subject Author Posted

deciding on a clip level?

Colm Connolly June 02, 2006 12:37PM

Re: deciding on a clip level?

Daniel Glen June 02, 2006 01:10PM