Random freesurfer commands and links

Table of surface areas (Desikan atlas)

aparc2statstable --hemi lh --subjects <list subjects> --tablefile lh.aparc.area.table

Table of thickness values (Desikan Atlas)

aparcstats2table --hemi lh --subjects <list subjects> -meas thickness --parc aparc --tablefile  lh.aparc.stats.thickness.table

Table of cortical volumes (Desikan Atlas)

aparcstats2table --subjects bert ernie fred margaret --parc aparc.a2005s --hemi rh --meas volume --tablefile aparc_stats_rh.txt

Table of subcortical volumes

asegstats2table --subjects bert ernie fred --meas volume --tablefile aseg_stats.txt

or create text file with path of all subjects and 

asegstats2table --subjectsfile=subject_to_write --meas volume --tablefile aseg_stats.txt

Change background of figure to white:

convert -fill white -opaque black <tksurfer_image_black_background>

<new_image_with_white_background>

http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/MorphAndRecon

Command line Group Analysis

https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis

Smoothing/qcache command

http://freesurfer.net/fswiki/FsTutorial/QdecGroupAnalysis_freeview

Methods citation

https://surfer.nmr.mgh.harvard.edu/fswiki/FreeSurferMethodsCitation

Check surfaces

tkmedit your_subject_name wm.mgz rh.white -aux brain.mgz \

tkmedit your_subject_name wm.mgz lh.white -aux brain.mgz

https://surfer.nmr.mgh.harvard.edu/fswiki/BasicReconstruction

Check subcortical segmentation
tkmedit SUBJECT orig.mgz -aux-segmentation aseg.mgz

Explanation of steps of reconstruction
http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/MorphAndRecon

Recon-all descriptions
https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all