-
Preprocessing is a key aspect in MRI analyses. There is not a gold standard to achive a "good" preprocessing of MRI data, neither in humans, macaques or any other species.
-
Each PRIME-DE site collected macaque fMRI in a different way (e.g Field of View, voxel resolution etc.).
-
between-site discrepancies in data acquisition result in the need of creating customized and flexible AFNI scripts to address different issues in the data that vary from site to site.
-
We are trying to generate a customized AFNI preprocessing recipe for each PRIME-DE site (or in some cases per individual) to end up with the best possible quality of data.
a) Depending on your system features follow the installation guide . Also, make sure to install NMT atlases with @Install_NMT
b) If you are familiar with singularity/docker you can use our singularity recipe to build a container with a complete installation of AFNI:
-
Clone this repository with
git clone -
navigate to the utils folder:
cd utils -
Use the recipe to build the container:
sudo singularity build -F afni.sif build_afni_singularity_container |& tee singularity_build_afni.logs -
keep the container up to date. You can adapt the
utils/update_afni_container.shto set your set your specific paths properly.
Note: you must have root privileges unless you call singularity build with the --fake-root or --remote flags.