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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Lisa_Ka
April 16, 2015 08:50AM
Hey,

I am very new to working with AFNI and I hope you can help me. I have an input FSL cluster image which I want to apply as a mask onto a dataset to compute the average of all the voxels in specific clusters. Yet some of the clusters are huge so I would like to define a region of interest around the maximal activation of the cluster and average the activation only in this part of the cluster. I try to do it this way:

3dmaskave -mask /my_path_to_the_cluster/clusterIndex.nii.gz -quiet -xball -57 -30 36 10 /my_path_to dataset.nii.gz > /my_path_to_output.txt

The error I get is

5231 voxels survive the mask
++ 57 voxels in the boxes+balls
** FATAL ERROR: No voxels in the mask INTERSECT boxes+balls!

which I eventually am able to overcome if I increase the radius of the ROI. I just don't understand why wouldn't the defined sphere intersect with the cluster if it is literally defined inside of it. Does someone have an idea of whyit happens?
Thanks!

Lisa
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Subject Author Posted

specifying a spheric ROI inside a mask in 3dmaskave yields error

Lisa_Ka April 16, 2015 08:50AM

Re: specifying a spheric ROI inside a mask in 3dmaskave yields error

rick reynolds April 16, 2015 09:07AM