https://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction
Once all data is downloaded from dougal and transferred to your account (converted to NIFTI or not) you can start to set up the data for reconstruction.
1. Create a subdirectory for your raw data.
2. Create subject data directories with the following command:
recon-all -i ./SAGA/SAGA01/NIFTI/MPRAGE.nii.gz -subjid NAME_OF_OUTPUT_DIRECTORY
This specifies where to find the raw data, and what to name the new directory. This new directory will be empty except for 001.mgz (raw data), and this is where all processing data will be saved.
Running the reconstruction:
recon-all -all -subjid NAME_OF_OUTPUT_DIRECTORY
