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

History of AFNI updates  

|
March 05, 2015 02:12PM
The lobe or just the anterior part of the temporal lobe is not available as such in any of the atlases that are distributed with AFNI, however the regions that make up that area are included under various names. If you need the ATL, you can make a composite region with 3dcalc like this:

3dcalc -a TT_Daemon::Right_Transverse_Temporal_Gyrus -b TT_Daemon::Right_Superior_Temporal_Gyrus \
-c TT_Daemon::Right_Inferior_Temporal_Gyrus -d TT_Daemon::Right_Middle_Temporal_Gyrus \
-expr 'step(a+b+c+d)' -prefix right_temporal_gyrus

This command uses an atlas defined for Talairach space (and just combines the overall right temporal gyrus). If your data is in another space, like MNI, you may want to either transform the composite mask to MNI space or the subject datasets to Talairach space. There are several other posts on how to do this. Also consider using other atlases to see other neuroanatomical subdivisions. For instance, the Talairach Daemon used above also contains the Brodmann areas that has also been used in the past to define the ATL.

Explore the distributed atlases by opening afni in your afni distribution directory (e.g. afni ~/abin). Atlas labels can be shown in the lower right of the overlay panel, or right click on the image viewer to show labels in that window. You can also look at which atlas regions are available on the command line with "whereami -show_atlas_code" or search for approximate matches with apsearch.

whereami -show_atlas_code > all_atlas_area_names.txt
apsearch -file all_atlas_area_names.txt -word hipp \
-min_different_hits 5 -unique_hits_only
Subject Author Posted

Extracting ROI from pre-proccessed data using brain area name

sdb99 March 04, 2015 05:44PM

Re: Extracting ROI from pre-proccessed data using brain area name

Daniel Glen March 05, 2015 02:12PM