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PRIME-DE preprocessing with AFNI

Description:

  • 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.

General Preprocessing steps

1. Install AFNI.

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.sh to 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.