I am a noob of brain data analysis , i am wondering how to use AAL3 altas in AFNI ,i would appreciate if there are any details
Howdy-
You just need to have the file on your computer, either in the directory you want to use or in the directory defined by your AFNI_ATLAS_PATH.
What would you like to do with the atlas? Visualize/overlay? Calculate ROI stats? Include in your processing?
You might also be interested in the AFNI Academy set of videos, from our Bootcamp teaching.
–pt
Thanks I would like to Calculate ROI stats，and Could u help me get more datails about how to operate AFNI_ATLAS_PATH ，I just download AAL3v1_for_SPM12.zip for website and I have no idea about how to operate the file 。
Hi-
This AFNI Academy video discusses ROI calculation tools, like 3dROIstats, and the online program help is here.
From the filename you mentioned, “AAL3v1_for_SPM12.zip”, you probably have a directory to unpack via:
unzip AAL3v1_for_SPM12.zip
See what file in there you want to use. You can copy that file to your directory that has other datasets, and use it then.
Or, you can define a special directory on your computer for all reference datasets, so whenever you use the AFNI GUI, it will check there. Let’s say you define a directory called /home/some_name/REF_DATASETS. If you have a different path to it on your computer, put that path, below.
If you have fully set up AFNI on your computer, you should have a runtime settings file called ~/.afnirc (note the dot at the start of the name). You can open it with any text editor. You can use an AFNI command to choose a text editor that is available on your computer:
afni_open -e ~/.afnirc
If you don’t have that file, then that means you haven’t completely set up AFNI on your computer. Installation instructions are here for any OS. You can also specifically run the system check to see what is missing:
afni_system_check.py -check_all
Look at the “Please fix” section at the bottom, which will have suggestions about what you need to do, and gives you a copy+paste command to create the ~/.afnirc files specifically.
So now I will assume you have that file, which holds all your possible AFNI environment variables. Again, you can use afni_open -e ~/.afnirc to open it. Then go to the bottom and set the relevant pointer to your reference data directory; let’s actually set 2 variables with the same info, by putting these 2 lines at the bottom:
AFNI_ATLAS_PATH = /home/some_name/REF_DATASETS
AFNI_GLOBAL_SESSION = /home/some_name/REF_DATASETS
After that, the next time you run the AFNI GUI, you should see the datasets there available to be selected for underlay/overlay. Commands referencing datasets in those directories should also find them.
To use 3dROIstats, please see the help file above. You will import your ROI dataset, and another dataset whose information you want to estimate statistics of. You have to make sure those datasets are on the same grid, to be able to command line calculations with them. To see if they are on the same grid, run:
3dinfo -same_all_grid DSET1 DSET2
A set of five 1s being output means they are, and a set of five 0s means they aren’t. See the online 3dinfo help file (or run 3dinfo -hview) for what the five properties being compared are.
A basic example of 3dROIstats is:
3dROIstats -mean -mask DSET_AAL DSET_TIMESERIES
–pt