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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Zhihao Li
October 04, 2007 05:35PM
Hi AFNI experts,

As the spatial smooth should be only applied on voxels within the brain, I'm wondering if the "3dmerge -1blur_fwhm"
has already included some auto-masking mechanisms.

I noticed there is a -1fmask option in the 3dmerge command, but it only affects -1filter_* and -t1filter_*, so we can not explicitly apply mask in the "3dmerge -1blur_fwhm".

I also noticed that we can do brain-masked spatial smooth via 3dBlurToFWHM, but this blur considers the intrinsic smoothness from the data.

There was an old discussion on this board about doing brain-masked blur without considering the intrinsic data smoothness by using a combination of -1fmask and -1filter_expr in the 3dmerge command (http://afni.nimh.nih.gov/afni/community/board/read.php?f=1&i=20919&t=20844#reply_20919). However, the discussion seems inconclusive.

So I got my question as posted in the title. If the answer is no, how do we add the brain mask?
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Subject Author Posted

Does 3dmerge -1blur_fwhm has brain mask?

Zhihao Li October 04, 2007 05:35PM

Re: Does 3dmerge -1blur_fwhm has brain mask?

Daniel Glen October 12, 2007 12:14PM

Re: Does 3dmerge -1blur_fwhm has brain mask?

bob cox October 12, 2007 01:12PM