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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February 09, 2004 02:54PM
3dAutomask first finds the 3dCliplevel value. It then clips the data (like your 3dcalc command). It proceeds with some extra steps:

- keeping only the largest above-threshold cluster of nonzero voxels in this mask
- filling in any small holes in that mask
- eroding off any loosely connected regions in the mask
- redilating any closely connected regions that were lost in the erosion

You should look at the two masks, but you will probably prefer the 3dAutomask generated dataset. If you think it is a little too small, you can dilate it outwards with the -dilate option.

Zorkon the Masked
Subject Author Posted

motion correction

Lucy Qiu February 09, 2004 01:31PM

Re: motion correction

bob cox February 09, 2004 01:53PM

Re: motion correction and Mask

Lucy Qiu February 09, 2004 02:48PM

Re: motion correction and Mask

Robert Cox February 09, 2004 02:54PM

Re: motion correction

Ricky Tong November 09, 2005 11:36AM

Re: motion correction

yi November 10, 2005 10:39AM

Re: motion correction

Godot November 10, 2005 10:57AM

motion correction using 3drotate with -1Dfile

Ricky Tong November 11, 2005 10:32AM

Re: motion correction using 3drotate with -1Dfile

Godot November 13, 2005 11:31PM

Re: motion correction using 3drotate with -1Dfile

Ricky Tong November 16, 2005 10:51AM

Re: motion correction

bob cox November 16, 2005 11:38AM