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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bob cox
November 03, 2003 11:47AM
You can form a mask dataset from connected clusters of above-threshold voxels by doing something like
3dmerge -dxyz=1 -1clust_order 1 10 -1thresh 4.5 -1tindex 13 -1dindex 13 -prefix zork_mask -datum short zork+orig
which will threshold sub-brick 13 at level 4.5, then form clusters of these voxels, assign the largest cluster the index 1, the next largest index 2, etc.
You can then use 3dmaskave or 3dROIstats to extract averages over these mask regions. Alternatively, you can create masks manually using the "Draw Dataset" plugin.

If you want percent change or some quantity NOT calculated by 3dDeconvolve, you have to first calculate that, perhaps using 3dcalc. You can search this message board for previous posts on that subject.

bob cox
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Subject Author Posted

stats of activated area

george he October 31, 2003 04:40PM

Re: stats of activated area

bob cox November 03, 2003 11:47AM