Welcome to the ENIGMA-infra FreeSurfer 7 guidelines!

Prerequisites

This guide assumes that you have:

• installed Nipoppy and organized your data in BIDS
• Apptainer available as container platform

Pull container

We will apply the FreeSurfer functionalities that are included in the fMRIPrep pipeline. You can pull the fMRIPrep container in the following way:

apptainer build fmriprep_24.1.1.sif \
                    docker://nipreps/fmriprep:24.1.1

Make sure that you store the container in the containers folder that is referenced in your global config file.

For more information on fMRIPrep, see the fMRIPrep documentation.

Set up configuration

Next, we will need to install the fMRIPrep pipeline within Nipoppy. You can do this by simply running:

nipoppy pipeline install --dataset <dataset_root> 15427833

15427833 is the Zenodo ID for the Nipoppy configuration files for fmriprep 24.1.1. Read more about this step here.

Once the pipeline is installed, open the global config file and check whether the correct fMRIPrep version is included under PIPELINE_VARIABLES. The following paths should be replaced here under the correct version of the fMRIPrep pipeline in the global config file: - <FREESURFER_LICENSE_FILE> (required to run FreeSurfer; you can get a FreeSurfer licence for free at the FreeSurfer website) - <TEMPLATEFLOW_HOME> (see here for more info on Templateflow)

Run pipeline

Finally, simply run the following line of code:

nipoppy process --pipeline fmriprep --pipeline-version 24.1.1 --dataset <dataset_root>

This should initiate the FreeSurfer 7 segmentation of your T1-weighted images! You can also do a dry-run first by adding --simulate to your command. See all nipoppy process options here

Note: the command above will run all the participants and sessions in a loop, which may be inefficient. If you're using an HPC, you may want to submit a batch job to process all participants/sessions. Nipoppy can help you do this by: 1. generating a list of "remaining" participants to be processed for your job-subission script: nipoppy process --pipeline fmriprep --pipeline-version 24.1.1 --dataset <dataset_root> --write-list <path_to_participant_list> 2. automatically submitting HPC jobs for you with additional configuration (more info here)

Track pipeline output

The nipoppy track-processing command can help keep track of which participants/sessions have all the expected output files for a given processing pipeline. See here for more information.

nipoppy track-processing --pipeline fmriprep --dataset <dataset_root>

Running this command will update the processing_status.tsv under the derivatives folder.

Extract pipeline output

For automatic extraction of the cortical thickness, cortical surface area and subcortical volume into .tsv files, you can use another Nipoppy pipeline, called fs_stats. The Zenodo ID for this pipeline is 15427856, so you can install it with the following command:

nipoppy pipeline install --dataset <dataset_root> 15427856

Remember to define the freesurfer license file path in your global config file under the newly installed pipeline. Then, you can simply run

nipoppy extract --pipeline fs_stats --dataset <dataset_root>

to get things going. You can find the extracted data under <dataset_root>/derivatives/freesurfer/7.3.2/idp/.

Did you complete all FreeSurfer 7 processing and data extraction? Great job! You can now move on to the subsegmentation, or go straight to quality control.