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Freesurfer released a patch to Freesurfer 5.0 and 5.1 (https://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), which, among other effects, was found to alter the ICV value up to 20%. The following steps were taken to patch the CNDA Freesurfer pipeline on the 10th of December 2012. All previously run Freesurfer 5.0 and 5.1 sessions on the CNDA were patched directly (or will be--as of 10 December 2012, we're still in the process of patching) .

Issues Covered by Patch
1. The code to generate the SupraTentorial volume in aseg.stats was incorrect (generally yields volumes that are too high). A fixed linux version was obtained from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux and copied into $FREESURFER_HOME/bin/mri_segstats.

2. The mri_label2vol was found to exclude the last label. The fixed linux version was obtained from ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_label2vol and copied to $FREESURFER_HOME/bin. (This is a tool not currently used by the CNDA Freesurfer Pipeline).

3. The recon-all now runs the talairach stage (creation of talairach.xfm) before the nu_correct stage (creation of nu.mgz) because creation of nu.mgz now makes use of the talairach.xfm file (to roughly identify white matter for intensity scaling purposes). the implication of this change is that the talairach stage now takes orig.mgz as input (instead of nu.mgz) which may lead to tal-check failures on some data. the workaround is to add the flag -use-mritotal to the end of recon-all in order to run an alter talairach method (MNI's mritotal). in the next release of freesurfer, this will be run automatically if tal-check fails, but more importantly, in the next release, nu_correct will run on orig.mgz to create orig_nu.mgz which will be used as input to the talairach stage (after which orig_nu.mgz will be deleted). It may also be the case that the ICV (eTIV) calculation is inaccurate, due to a poor quality talairach alignment (which might none-the-less be suitable for the recon to work). The workaround is to run the following commands which will update the aseg.stats file with a new more accurate ICV value.
cd subjid/mri
talairach_avi --i nu.mgz --xfm transforms/talairach.xfm
recon-all -s subjid -segstats
recon-all -s subjid -wmparc

Files Affected by the Patch
scripts/build-stamp.txt
scripts/recon-all.env
scripts/recon-all.log
scripts/recon-all.done
scripts/csurfdir
scripts/recon-all-status.log
scripts/recon-all.local-copy
scripts/recon-all.cmd
scripts/ponscc.cut.log
scripts/hippo-subfields.log
stats/aseg.stats
stats/wmparc.stats
mri/transforms/talairach_avi.log
mri/transforms/talairach.xfm
mri/transforms/talsrcimg_to_711-2C_as_mni_average_305_t4_vox2vox.txt
mri/wmparc.mgz