Hello Freesurfer team, I've been previously learning freesurfer by going through the individual recon-all commands listed on the freesurfer website v5.3 table here: http://freesurfer.net/fswiki/ReconAllTableStableV5.3 and recently just ran through the recon-all autorecon steps 1, 2 and 3.
Running the command individually as listed on the website: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --etiv --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/FreeSurferColorLUT.txt This produces both cortical and subcortical volumetric data in the same wmparc.stats file. (attached to this email as wmparc.stats) Whereas, the default command from recon-all is: mri_segstats --seg mri/wmparc.mgz --sum stats/wmparc.stats --pv mri/norm.mgz --excludeid 0 --brainmask mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm --in-intensity-units MR --subject TB0204U_FREESURFER_THIRDRUN --surf-wm-vol --ctab /usr/local/freesurfer/WMParcStatsLUT.txt --etiv The resulting file is attached to this email as wmparc2.stats along with the DK40 stats. The only differences are the --brain-vol-from-seg flag (which doesn't seem relevant, based on the description of the flag), and the lookup table used in the generation of the wmparc.stats file. During the recon-all run, the wmparc.stats file only listed subcortical regions, whereas the DK40 atlas is the only source listing cortical volumes. While I would just use the DK40 atlas to retrieve this information, the problem here is that there appears to be a significant difference between the mm^3 volume of hemispherical cortical areas listed in the DK40 atlas compared to those produced when running the command with the flags. Unfortunately, I am not familiar enough with cortical volumes to recognize which estimate is more reasonable one. What .stats file or look-up table should I be using to obtain the most accurate cortical data? Also, when fixing errant ROI label voxels with freeview voxel editor, what commands need to be run post-editing to apply the corrections? I was under the impression that the aparc+aseg.stats file was edited when changing the ROIs. Although, I was rather confused when I went back and regenerated the aparc+aseg.mgz file and my edits were still present. Best, -Kody J. Zalewski
wmparc.stats
Description: Binary data
wmparc2.stats
Description: Binary data
lh.aparc.DKTatlas40.stats
Description: Binary data
rh.aparc.DKTatlas40.stats
Description: Binary data
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