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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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Kristi Clark
August 14, 2003 05:52PM
Hi. I have a question about how 3dFWHM uses a mask file. This is what I have done with some interesting (?) results:

Input files:
1. Funcfile+orig.BRIK (1 functional image, 64x64x32): data has range from 0 to 1012.
2. Graymatter_mask+orig.BRIK (a gray matter mask, 64x64x32): I created this mask file outside of afni, and then converted it to afni format. It has a value of 1 for gray matter, and a value of 0 everywhere else.

Calculations performed:
1. 3dFWHM -dset Funcfile+orig.BRIK
FWHMx = 41.53
FWHMy = 47.68
FWHMz = 30.66

2. 3dFWHM -dset Funcfile+orig.BRIK -mask Graymatter_mask+orig.BRIK
FWHMx = 20.83
FWHMy = 23.18
FWHMz = 13.99

3. 3dcalc -a 'Funcfile+orig.BRIK -b 'Graymatter_mask+orig.BRIK -expr 'step(B)*A' -prefix Funcfile_gray
3dFWHM -dset Funcfile_gray
FWHMx = 4.99
FWHMy = 5.12
FWHMz = 5.68

4. 3dcalc -a 'Funcfile+orig.BRIK -b 'Graymatter_mask+orig.BRIK -expr 'step(B)*A' -prefix Funcfile_gray
3dFWHM -dset Funcfile_gray -mask Graymatter_mask+orig.BRIK
FWHMx = 0.00
FWHMy = 0.00
FWHMz = 1.74

The results of calculation #1 make sense compared to the rest. However, I would have thought that calculations #2 & #4 would have been equal. So my question is first of all, how does 3dFWHM use a mask? Is it true that when calculating the smoothness of dset, only those voxels which have a value of 1 in the mask file are used in the calculation? My other question is which one of these calculations (Steps 2-4) are correct for estimating the smoothness of my functional image in the gray matter?

Thanks,
Kristi Clark
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3dFWHM & mask

Kristi Clark August 14, 2003 05:52PM