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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Daniel Glen
March 17, 2006 11:25AM
This shouldn't be too difficult with the 3dcalc command or the 3dmerge command. 3dmerge has options for thresholding and clustering. When you say each slice, how is this different from thresholding on each voxel?

With 3dmerge, use the -1thresh and -1clust options.

3dmerge -1thresh 0.5 -1clust 2 200 -1tindex 4 -prefix cl_thr -doall dataset+orig

Here the threshold is applied to allow only voxels over a value of 0.5 from sub-brick 4 with clusters of radius of at least 2mm and a volume of 200 ul.
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Subject Author Posted

3dDeconvolve output

katrina March 17, 2006 12:43AM

Re: 3dDeconvolve output

Daniel Glen March 17, 2006 11:25AM

Re: 3dDeconvolve output

katrina March 17, 2006 01:58PM