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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Dave
March 23, 2010 10:35AM
I've used 3dAutomask successfully in the past but just now when I tried to run the command

3dAutomask -prefix localizer_mask -SI 130 scaled_run1+orig I got no voxels clipped and the following output:

++ Loading dataset scaled_run1+orig
++ Forming automask
+ Fixed clip level = 0.000000
+ Used gradual clip level = 0.000000 .. 0.000000
+ Number voxels above clip level = 166400
+ Clustering voxels ...
+ Largest cluster has 166400 voxels
+ Clustering voxels ...
+ Largest cluster has 166400 voxels
+ Clustering voxels ...
+ Largest cluster has 166400 voxels
+ Clustering non-brain voxels ...
+ Clustering voxels ...
+ Largest cluster has 0 voxels
+ Mask now has 166400 voxels
++ 166400 voxels in the mask [out of 166400: 100.00%]
++ first 0 x-planes are zero [from R]
++ last 0 x-planes are zero [from L]
++ first 0 y-planes are zero [from A]
++ last 0 y-planes are zero [from P]
++ first 0 z-planes are zero [from I]
++ last 0 z-planes are zero [from S]
++ CPU time = 0.910000 sec

Can someone give some insight into what might be wrong?

Thanks!
Subject Author Posted

3dAutomask not

Dave March 23, 2010 10:35AM

Re: 3dAutomask not

rick reynolds March 23, 2010 11:25AM

Re: 3dAutomask not

Dave March 23, 2010 12:16PM

Re: 3dAutomask not

bob cox March 23, 2010 01:42PM