Run Freesurfer using the LONI Pipeline

T1 image with freesurfer aseg image overlaid

Written by Owen Phillips. Email Dr. Katherine Narr if you have any questions. For more information, see the protocols page.


  1. This protocol is set up to run two pipeline modules. Each one references a simple script which will run through the Freesurfer Processing. Download the pipeline modules Freesurfer_recon_all_Prep & Freesurfer_recon_all by right clicking the files.
  2. Open the Freesurfer_recon_all_Prep.pipe in the Loni Pipeline.
  3. Add the full path to your subject image data where it says Input Images.
  4. Add the subject IDs to the input module that says Subject IDs. It is important to maintain the same order as your input images. The output files will be named based on this input.
  5. Add the Subject Directory. This will be the output directory for your data.
  6. Click the Play button. It's not doing much, so it will run quickly as long as the grid isn't backed up.
  7. Open the Freesurfer Runner Pipeline.
  8. Input your images, Subject IDs and Subject Directory. You want this to be the same as the previous pipeline.
  9. Click Play. It will take about 24 hours to run, depening on how busy the Grid is.