ABIDE processing

I want to perform preprocessing steps from FREESURFER recon_all on ABIDE data which is in NIFTI format.

Can I run it directly on the data?
Or are there steps to be taken first? For example, convert NIFTI to mgz
Or restructure the folders??
I am a beginner in the neuroimaging field, any advice I would be grateful to you


  1. Yes, you can run recon-all on the data
  2. No, you do not have to convert from .nii to .mgz. You can pass in a .nii file into the -i argument of recon-all (see the documentation here)
  3. You do not have to restructure folders (they should already be in BIDS format)

Since the data folders are already in BIDS format, you can also look into running sMRIPREP, which is a comprehensive anatomical preprocessing pipeline that includes FreeSurfer. Also, ABIDE I already has preprocessed derivatives available, including FreeSurfer.