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  

August 13, 2015 06:08PM
I am very pleased to announce the Waxholm rat atlas is now available to the AFNI community and others, courtesy of the authors of Papp et al. 2014 and Kjonigsen et al. 2015. This rat template and atlas are provided at the original resolution - a stunning 39 micron cubic voxel! The dataset is available here for download.

In order to use this atlas relatively seamlessly, modify your .afnirc file like this:

AFNI_SUPP_ATLAS_DIR = ..../ratbrain

Change the path for the supplemental atlas directory listed above to the path where the directory and the template actually are installed. With these few changes, AFNI will use the Waxholm rat atlas with whereami.

The template provided here is a skullstripped version that has been compressed to byte data to save memory. The atlas is slightly different from the original in that it has been modally smoothed and saved in byte format. Both the template and atlas should be more appropriate for MRI and FMRI use than the datasets directly available from the INCF Waxholm site. The template is also provided at half resolution, still a respectable 78 um, in order to be more easily used with other MRI datasets. Additionally, surface datasets are available for each of the regions included in the atlas. The original data, untouched by me, is available here:

As a pretty example, here are a few hippocampal structures selected and shown as separate surfaces in suma with this command. The CA1 region is shown transparently.

suma -onestate -i waxrat.cornu*.gii waxrat.dentate*.gii waxrat..entorhinal*.gii waxrat.*hippo*.gii waxrat.*subiculum*.gii &

The effort by the authors was significant, so please cite them appropriately. The citation references are available via the "whereami -show_atlases" command and here:

For the overall atlas, the paper to cite is:
Papp EA, Leergaard TB, Calabrese E, Johnson GA, Bjaalie, JG (2014) Waxholm Space atlas of the Sprague Dawley rat brain. NeuroImage 97, 374-386

For the hippocampal region, please cite:
Kjonigsen LJ, Lillehaug S, Bjaalie JG, Witter MP, Leergaard TB (2015) Waxholm Space atlas of the rat brain hippocampal region: Three-dimensional delineations based on magnetic resonance and diffusion tensor imaging. NeuroImage 108, 441–449

Edited 1 time(s). Last edit at 09/04/2015 02:54PM by Daniel Glen.
Subject Author Posted

Rat atlas announcement

Daniel Glen August 13, 2015 06:08PM

Re: Rat atlas announcement

Emperor Zhark August 14, 2015 09:25AM

Re: Rat atlas announcement

Ziad Saad September 03, 2015 05:35PM

Re: Rat atlas announcement

Ziad Saad September 04, 2015 01:45PM

Re: Rat atlas announcement

Daniel Glen September 04, 2015 03:47PM

Re: Rat atlas announcement

jimmy601521 May 29, 2017 01:48PM

Re: Rat atlas announcement

ptaylor May 29, 2017 04:31PM

Re: Rat atlas announcement

jimmy601521 May 29, 2017 10:00PM