Learning notes on how to use freesurfer to analyze structural data

• See example T1_organize.sh

• Use the FS_preprocess.sh
• View the results with freeview

• Create three folders, FS, FSGD, Contrasts
• Put all output data into FS
• Creat FSGD file (.fsgd) under FSGD
• Creat Contrast file (.mtx) under Contrasts

with mris_preproc

with mri_glmfit

with mri_glmfit-sim

Introduction to Freesurfer Output

Video Part I Part II

? was often used to represent left or right

It includes labels of several brain atlas, such as

  ?h.apar.DKTatlas.annot  >>> Desikan-Killiany atlas

  ?h.aparc.a2009s.annot >>> Destrieax atlas

compasses all the volume data

  raw_avg.mgz >>> the raw volume data in raw space resolution

  others >>> in the normalized space

it contains the scripts or logs when it goes through processing

  recon-all.log  >>> the log file you can go through if there is something wrong

contains the statistics of the brain, such as the thickness or volume of different brain regions.

includes all the surface files

  ?h.orig & ?h.white >>> the boundary between the white matter and the grey matter

  ?h.pial >>> the boundary between the grey matter and the pia matter

  ?h.inflated >>> inflated brain 

  ?h.thickness or ?h.volume >>> values of the thickness or volume projected onto the inflated brain

Volume space: native volume and MNI space;

  MNI space (MNI152NLin2009cAsym-fMRIprep; MNI152NLin6Asym-FSL);

Surface space: native surface (generated from freesurfer) and standard surfaces (fsaverage; fsLR file formate CIFTI)

  fsaverage (fs3>>1k; fs4>>3k; fs5>>10k; fs6>>41k; fs7>>164k); per hemisphere
  fsLR (fsLR32k; fsLR164k) per hemisphere 

from native > native surface> fsaverage > fsLR (This is the recommended procedure to project to fsLR space)

?.sphere.reg is the registration file from native surface to fsaverage

How to project from native to fsaverage and to fsLR

toolbox based on matlab

mri_vol2surf >> from volume data to surface data
mri_surf2vol >> from surface data to volume data
mri_surf2surf >> from surface to surface, standardize or downsample or upsample (i.e. native to fs; fs to fs5)

Wu J, Ngo GH, Greve DN, Li J, He T, Fischl B, Eickhoff SB, Yeo BTT. Accurate nonlinear mapping between MNI volumetric and FreeSurfer surface coordinate systems, Human Brain Mapping 39:3793–3808, 2018.

The two methods mentioned above can only convert the data from the MNI to fsaverage, and within fsaverage, but can not project into fsLR format.

Markello, RD, Hansen, JY, Liu, ZQ, Bazinet, V, Shafiei, G, Suarez, LE, Blostein, N, Seidlitz, J, Baillet, S, Satterthwaite, TD, Chakravarty, MM, Raznahan, A, Misic, B. (2022). neuromaps: structural and functional interpretation of brain maps. Nature Methods. doi:10.1038/s41592-022-01625-w

https://netneurolab.github.io/neuromaps/user_guide/atlases.html