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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Erin Harral
January 31, 2006 03:45PM
We're coming across an error when we cluster threshold some of our data. Here is what we are doing:

1) 3dSkullStrip individual brains from each condition

2) apply mask to individual functional effect size maps using mri_rpn_math

3) run 3dttest on brains from each condition

3dttest output maps come out fine. When we change the scale and apply color to near but non-zero values, we still see no activation, no artifact. It looks good.

4) 3dmerge to cluster threshold the maps at p=.01 and p=.001.

After the cluster thresholding procedure, we find artifact outside of the brain that resembles tiny grids/dotted lines.

Skull stripping *should* have masked out any activation outside of the brain. We also find it odd that the artifact does not appear present on any of the raw data or maps in earlier steps in processing. Any ideas? -Erin

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Subject Author Posted

artifact outside of brain

Erin Harral January 31, 2006 03:45PM

Re: artifact outside of brain

Ziad Saad February 02, 2006 11:39PM

Re: artifact outside of brain

Erin Harral February 06, 2006 02:59PM