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  

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June 15, 2017 11:35AM
That atlas is popular with SPM. I looked at this a couple years ago and found, it is almost identical to the Eickhoff-Zilles Macro-label atlas based on the N27 dataset that is already included with AFNI. There are minor differences, but I'm sure they won't be too important. You can judge for yourself with a few commands.

# I've got the datasets I need in an old mricron directory
cd /Users/dglen/mricron/mricron.app/templates/
# afni can always use this directory for atlases
setenv AFNI_SUPP_ATLAS_DIR `pwd`
# the last empty line confuses the @Atlasize script, so remove that line
head -116 aal.nii.txt > fixed_aal.nii.txt
# add -G if you want to make this atlas show up with all other atlases (try it first in place)
@Atlasize -space MNI -lab_file fixed_aal.nii.txt 1 0 -dset aal.nii.gz

# compare with the ML macrolabel and MPM atlas from Eickhoff-Zilles
cp ~/abin/MNIa_caez_m*_18+tlrc.* .
@Shift_Volume -MNI_Anat_to_MNI -prefix MNI_caez_ml_18 -dset MNIa_caez_ml_18+tlrc.
# use the GUI to compare - underlay, overlay, multiple controllers
afni

You will notice that the shift of MNI_anat to MNI doesn't produce exactly the same thing. There's about a 1mm shift in two directions, and a couple regions are very slightly different. Still both the ML and AAL datasets are obviously from the same source. Consider the other atlases like the MPM and the Desai atlases made from Freesurfer segmentation. Also take a look at the other MRIcron atlases. If there's one you want, it's usually not more than the few steps above.
Subject Author Posted

Extracting ROI signals using AAL atlas

heretic133 June 15, 2017 03:37AM

Re: Extracting ROI signals using AAL atlas

Daniel Glen June 15, 2017 11:35AM

Re: Extracting ROI signals using AAL atlas

heretic133 June 16, 2017 02:38AM

Re: Extracting ROI signals using AAL atlas

Daniel Glen June 16, 2017 10:23AM