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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Daniel Glen
March 23, 2006 01:53PM
One thing to keep in mind here is 3dUndump is making a dataset with a single number for each cluster. The number is set by the value placed in the clustcoords.1D serial column. If the clusters overlap, you will only have the last cluster number. This may not be a problem in this particular case because this problem concerns only a minimal size sphere from a group of distinct clusters. But if the clusters were very skinny, then it is possible one cluster could overlap another.

For overlapping clusters, it would probably be better to use 3dUndump to create multiple mask files, a separate mask in each dataset. There is an interesting discussion of part of this problem using 3dcalc from an old message board posting:

[afni.nimh.nih.gov]
[afni.nimh.nih.gov]
[afni.nimh.nih.gov]

Also to avoid calculating the sphere regions outside the brain you will probably want to combine the 3dUndump with the -mask option.
Subject Author Posted

constraining cluster size for 3dmaskave

Agatha March 22, 2006 05:19PM

Re: constraining cluster size for 3dmaskave

Daniel Glen March 22, 2006 05:51PM

Re: constraining cluster size for 3dmaskave

Agatha March 22, 2006 06:01PM

Re: constraining cluster size for 3dmaskave

Daniel Glen March 23, 2006 11:01AM

Re: constraining cluster size for 3dmaskave

Daniel Glen March 23, 2006 01:53PM