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:

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

History of AFNI updates  

September 04, 2015 05:33PM
On behalf of Sam Torrisi, NIMH:

These probabilistic masks of the Bed Nucleus of the Stria Terminalis (BNST) are offered for fMRI-based analyses. Individual subject BNST masks were manually created by three raters from 7 Tesla, 0.7mm isotropic, T1 structural scans of 36 healthy adults. These datasets were nonlinearly warped using AFNI's 3dQwarp to the ICBM 2009b Nonlinear Asymmetric template (also called “MNI 152 nonlinear template”): . We therefore recommend the use of these BNST masks with this template for group studies. Whether you do use this template or not, it is still highly recommended to visually check your alignment; see figure and citation below for details of anatomical boundaries.

Figure 1: 50% probability map overlaid on high resolution MNI asymmetrical template. Coronal slices from anterior to posterior.

Figure 2: Same threshold, sagittal slice shows location of coronals slices above.

Download all masks from the following link:

Included in this distribution are these two datasets (with AFNI atlas attributes) :

probbnsts36.nii.gz: unthresholded mask (probabilistic maps stored as floats, left-right as separate sub-brick volumes)

bnsts36_50.nii.gz: Thresholded mask at 50%, stored as bytes.

If one wishes to add these to the whereami program in AFNI for automated identification, modify your .afnirc file like this:

AFNI_SUPP_ATLAS_DIR = ..../bnst_v1.0

Change the path for the supplemental atlas directory listed above to the path where the directory and the maps actually are installed on your system.

Direct questions and comments to Salvatore (Sam) Torrisi (sam.torrisi @ or Daniel Glen (glend @

Please cite:
Torrisi, S., O'Connell, K., Davis, A., Reynolds, R., Balderston, N., Fudge, JL., Grillon, C., Ernst, M (2015). Resting state connectivity of the bed nucleus of the stria terminalis at ultra-high field. Human Brain Mapping. Volume 36(10).

Special thanks to Daniel Glen (aw, shucks... DG)

Edited 2 time(s). Last edit at 09/04/2015 06:25PM by Daniel Glen.
Subject Author Posted

Bed Nucleus Stria Terminalis Maps

Daniel Glen September 04, 2015 05:33PM