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  

|
March 27, 2006 09:08AM
It DOES print out the clip level -- the 5th line of the sample output below:

% 3dAutomask anat+orig
++ Program 3dAutomask: AFNI version=AFNI_2006_03_21_1314 [32-bit]
++ Authored by: RW Cox
++ Loading dataset anat+orig
++ Forming automask
+ Clip level = 27.514389
+ Number voxels above clip level = 2091065
+ Clustering voxels above clip level ...
++ THD_mask_clust: building cluster ...
+ Largest cluster has 2085107 voxels
+ Eroded 498549 voxels
+ Restored 409817 eroded voxels
++ THD_mask_clust: building cluster ...
+ Largest cluster has 1992751 voxels
+ Filled 53585 voxels in small holes; now have 2046336 voxels
+ Filled 361562 voxels in large holes; now have 2407898 voxels
+ Eroded 111475 voxels
+ Restored 111273 eroded voxels
++ THD_mask_clust: building cluster ...
+ Largest cluster has 2407696 voxels
+ Clustering non-brain voxels ...
++ THD_mask_clust: building cluster ...
+ Largest cluster has 5718521 voxels
+ Mask now has 2407943 voxels
++ 2407943 voxels in the mask [out of 8126464: 29.63%]
++ first 28 x-planes are zero [from A]
++ last 17 x-planes are zero [from P]
++ first 70 y-planes are zero [from S]
++ last 0 y-planes are zero [from I]
++ first 0 z-planes are zero [from L]
++ last 0 z-planes are zero [from R]
++ Output dataset ./automask+orig.BRIK
++ CPU time = 15.840000 sec

Subject Author Posted

how to save voxels when you mask brain

Tracy Jill Doty March 19, 2006 08:14PM

Re: how to save voxels when you mask brain

Zhark March 20, 2006 10:31AM

Re: how to save voxels when you mask brain

Ziad Saad March 20, 2006 11:18AM

Re: how to save voxels when you mask brain

Tracy Jill Doty March 23, 2006 05:18PM

Re: how to save voxels when you mask brain

Daniel Glen March 20, 2006 11:34AM

Re: how to save voxels when you mask brain

Vincent Costa March 21, 2006 06:54PM

Re: how to save voxels when you mask brain

Zhark, Emperor March 21, 2006 07:10PM

Re: how to save voxels when you mask brain

Vincent Costa March 26, 2006 10:02PM

Re: how to save voxels when you mask brain

Zhark March 27, 2006 09:08AM

Re: how to save voxels when you mask brain

Vincent Costa March 27, 2006 11:05AM