Monkey Data And FreeSurfer

This page contains notes on how to process monkey data using Freesurfer.

For starters, Sebastian Moeller has provided a set of scripts which break-down the steps individually. This is necessary because the recon-all script, which is the wrapper utility normally used to process human data, is not setup to work with monkey data. Sebastians scripts will guide you from raw anatomicals to reconstructed surfaces. The process requires intensive manual intervention, in the case of using a single channel surface coil system, is probably not precise enough for morphometric analysis. Mainly the surfaces are used for display purposes (and some experimental surface based functional group analysis).

NOTE: These scripts were developed for use with FS v4.5, users have reported having some trouble runnning these scripts with FS v5.1.

This pipeline for monkey data fakes the resolution information in the volume headers so that FreeSurfer sees 1mm isotropic and does not resample the data to 1mm. This is done in order to preserve information in the volume which would otherwise be discarded when resampled, at least for macaque or smaller monkey scans. If you are using these scripts for morphometry please be aware that all length measurements are off by (1 / actual_isotropic_voxel_size). Area and volume measurements will be off as well, but this can be corrected for.

Per this email exchange about correcting for sphinx positioning, here are the scripts:

MonkeyData (last edited 2021-05-03 08:55:18 by DevaniCordero)