Shell scripts to run FreeSurfer's recon-all in parallel on multi-core machines.

FreeSurfer is a state-of-the-art neuroimaging software suite, and its recon-all pipeline supports the fully automated reconstruction of mesh representations of the human cortex from raw MRI scans.

However, running recon-all takes very long (12 - 20 h per subject on current hardware) and typically needs to be run for hundreds of subjects for a medium-sized neuroimaging study. This repo contains bash shell scripts which allow one to run the time-consuming FreeSurfer pre-processing in parallel on multi-core systems. The parallelization is done on the subject level, meaning that a single subject still takes a long time, but each core of your computer runs one subject. The main tool behind this is the GNU parallel software.

These scripts are mainly intended for running FreeSurfer on powerful workstation computers in a lab. They are not suitable for running FreeSurfer on high performance computing (HPC) clusters which use a job scheduler like Slurm.

No special hardware is required. You will obviously need a multi-core computer (almost all modern machines are multi-core, even laptops) that can run FreeSurfer and about 1.5 - 2 GB of free RAM per CPU core you want to use.

An example would be a quad-core computer with 12 GB of RAM (4x2 GB for FreeSurfer, leaving another 4 for the operating system and all other processes).

We run this on an AMD Threadripper Linux workstation with 48 cores, 128 GB of RAM and a fast SSD. I typically do not use all of the cores but leave 2 or 3 idle so that I can still use the computer for basic tasks while the pre-processing is running in the background.

• Any Linux or MacOS operating system that can run FreeSurfer
• A working FreeSurfer 6 or 7 installation (including proper setup for the bash shell)
• GNU parallel, which is used for parallelization in all of the scripts

If you start the commands on a remote workstation, e.g., via SSH, we strongly recommend to also install and use a terminal multiplexer like GNU screen on the remote computer so that the computations, which will take several days for large samples, will not abort if the network connection from your computer to the workstation gets lost for a second or you accidentaly close the terminal app on your local computer. This is optional though.

This involves running the recon-all pipeline, which takes 12 - 20h per subject. Typically qcache is also run as part of the pipeline, to map the resulting data (like per-vertex cortical thickness in native space) to standard space (fsaverage).

We recommend the following steps:

• First convert the raw DICOM files to NIFTI format using dcm2nii.
  • Note: If you have .nii.gz files, make sure to extract them to get .nii files. E.g., in bash: for nf in *.nii.gz; do gunzip "$nf"; done
  • Note: You may have more than one structural scan per subject at this time (e.g., if the first one was aborted or looked bad during scanning). That is fine, you have to pre-process both with FreeSurfer first to decide which one to use later.
• Use the script cross-sectional/preproc_reconall_parallel.bash from this repository to run recon-all for all NIFTI files in parallel.
  • Note: If you have TSE (or t2-weighted) files in addition to t1-weighted files, please adapt the cross-sectional/preproc_reconall_single_subject.bash script to make sure they are used during pre-processing.
• If you want to add a global brain measure (like total brain volume) as a covariate during modeling later, run the script tools/extract_total_brain_measures.bash to compute the measures for all subjects.

Note: If you will get data for a second wave later and intend to run a longitudinal analysis then, please read about the longitudinal pipeline now to avoid duplicate work later.

This requires first running the cross-sectional recon-all pipeline for all time points you have. If a subject is named subject1 and you have MRI scans from two time points, the NIFTI input files should be called subject1_MR1.nii and subject1_MR2.nii before you run the cross-sectional pipeline, so that you get two output directories named subject1_MR1 and subject1_MR2.

Then, you can run the longitudinal pipeline using the script ./longitudinal/fs_longitudinal_pipeline.bash from this repo. The script performs 3 tasks which can be run independently, and we recommend to run one after the other and check whether everything finished successfully before moving on to the next step. The 3 steps are:

1. Creating an inter-subject template brain from all scans / time points for each subject. Creates a directory named subject1.
2. Mapping the data from the time points (directories subject1_MR1 and subject1_MR2) to the template, creating directories subject1_MR1.long.subject1 and subject1_MR2.long.subject1.
3. Computing the change between the timepoints for one or several descriptors (cortical thickness, surface area, ...).

The first 2 steps use a subjects file, but part 3 requires a QDEC table in longitudinal format that holds information on the age of each subject at each timepoint, so that the inter-scan interval can be computed. If you have a more typical demographics table instead and need to create the QDEC file from that format, I recommend to use R. There is a function named demographics.to.qdec.table.dat in the fsbrain package that makes the tedious and error-prone conversion process a lot easier.

The tools directory contains many scripts to perform various tasks that frequently come up in computational neuroimaging. Have a look and see what's available. It includes scripts to:

• map data from native to standard space in parallel for many subjects
• downsample meshes for individuals
• compute local gyrification index (lGI) in parallel, both for cross-sectional and longitudinal data sets
• smooth per-vertex data in parallel
• generate mid surfaces (between the white and pial surface) in parallel
• apply an atlas available as an fsaverage parcellation to a subject (in native space)
• compute covariates / global brain measures like the total brain volume for your subjects and save them to a CSV table
• copy only certain files from a FreeSurfer SUBJECTS_DIR to a new directory tree while keeping the directory layout
• ...

See all scripts.

These can be found in the scripts, just open them with a proper text editor like Atom or vscode.

This does not mean that there are no good instructions. It's just that duplicating the docs on this website does not make any sense: it is very likely that I would forget updating the website when I change the scripts. I'm much more likely to adapt the instructions in the scripts when editing them.