Fixing of Morphometry Stats and Global Measure of Volume

On Apr 2, 2019, an error was discovered in FreeSurfer version 6 in the computation of some of the global metrics on high resolution data analyzed at high resolution (thanks to Antonin Skoch for finding the problem). The bug was that the reported values were in voxels not mm3. Any analyses where the input volumes were 1mm voxel size or were conformed to 1mm voxel size are NOT affected. Any analyses not using version 6 is NOT affected (eg, version 5.3 is NOT affected). The recent patch used by the HCP for high resolution surface placement is NOT affected because the volume analysis is done at 1mm.

Note that Estimated Total Intracranial Volume (eTIV) was not affected by this bug.

The affected measures are:

# Measure BrainSeg, BrainSegVol, Brain Segmentation Volume
# Measure BrainSegNotVent, BrainSegVolNotVent, Brain Segmentation Volume Without Ventricles
# Measure lhCerebralWhiteMatter, lhCerebralWhiteMatterVol, Left hemisphere cerebral white matter volume
# Measure rhCerebralWhiteMatter, rhCerebralWhiteMatterVol, Right hemisphere cerebral white matter volume
# Measure CerebralWhiteMatter, CerebralWhiteMatterVol, Total cerebral white matter volume
# Measure SubCortGray, SubCortGrayVol, Subcortical gray matter volume
# Measure TotalGray, TotalGrayVol, Total gray matter volume
# Measure SupraTentorial, SupraTentorialVol, Supratentorial volume
# Measure SupraTentorialNotVent, SupraTentorialVolNotVent, Supratentorial volume
# Measure Mask, MaskVol, Mask Volume
# Measure BrainSegVol-to-eTIV, BrainSegVol-to-eTIV, Ratio of BrainSegVol to eTIV
# Measure MaskVol-to-eTIV, MaskVol-to-eTIV, Ratio of MaskVol to eTIV
# Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume
# Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume
# Measure Cortex, CortexVol, Total cortical gray matter volume,

These values appear in some of the files in the subject/stats folder and are transferred using asegstats2table.

These measures are NOT affected

# Measure EstimatedTotalIntraCranialVol, eTIV, Estimated Total Intracranial Volume

This problem has been fixed and a patch put here. If this problem affects you, you will need to download new versions of mri_segstats and mris_anatomical_stats, copy them into $FREESURFER_HOME/bin. Get the one appropriate for you system labeled .linux or .mac. When you copy them, copy without .linux or .mac. Then run

recon-all -s subject -segstats -parcstats -parcstats2 -parcstats3 -wmparc -balabels

Stats files that have been run with the new programs will have either this line:

# BrainVolStatsFixed see surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed

or this line

# BrainVolStatsFixed-NotNeeded because voxelvolume=1mm3