afni hippocampus subfield atlas

AFNI Message Board
1

Hi afni experts,

I need a mask of the hippocampus subfield atlas, such as CA1, CA2, CA3, CA4, DG, Sub.
Do you know which atlas includes those in afni?

Thanks!
Taiping

2

The JulichBrain has all those except for CA4. You can find the JulichBrain in future releases of AFNI soon or find them here in both MNI_N27 and MNI_2009c template spaces.

https://afni.nimh.nih.gov/pub/dist/atlases/JulichBrain/

Current releases include some of the regions in the Eickhoff-Zilles architectonic atlases - the CA_MPM_22_MNI (MNI_N27 space), CA_MPM_22_TT (TT_N27 space). The corresponding file names are MNI_caez_mpm_22+tlrc. TT_caez_mpm_22+tlrc., usually found in the AFNI binary directory.

A good way to search for regions is by using (tcsh or zsh syntax)

whereami -show_atlas_code |& less

and searching with the forward slash key '/'. You can search a particular atlas a variety of ways. The lines that contain hippocampus are shown below for one of the JulichBrain atlases.

whereami -atlas Julich_MNI_N27 -show_atlas_code |grep Hippocampus
r:right_CA2_(Hippocampus):23
l:left_CA2_(Hippocampus):223
r:right_CA3_(Hippocampus):24
l:left_CA3_(Hippocampus):224
r:right_DG_(Hippocampus):26
l:left_DG_(Hippocampus):226
r:right_CA1_(Hippocampus):27
l:left_CA1_(Hippocampus):227
r:right_HATA_(Hippocampus):28
l:left_HATA_(Hippocampus):228
r:right_Subiculum_(Hippocampus):67
l:left_Subiculum_(Hippocampus):267
r:right_HC-Transsubiculum_(Hippocampus):111
l:left_HC-Transsubiculum_(Hippocampus):311