It seems that there is a serious error in the Parcellation stats files (i.e. ?h.aparc.stats) when using the FLAIR / T2 processing pipeline of FS 5.3. 

starting a particular recon-all with 

    recon-all -s ${SUBJID} -i ${DIR} -FLAIR ${DIR/t1/flair} -FLAIRpial -all

and looking through the recon-all.cmd file, it appears that the Parcellation stats are computed prior to refining the pial surfs, but not updated after refining the pial surfs.

For instance: 

#@# Parcellation Stats lh Thu May 29 14:36:50 CEST 2014

and further on:

#@# Refine Pial Surfs w/ T2/FLAIR Thu May 29 15:36:58 CEST 2014

but mris_anatomical_stats is not called again after updating the pial surfs. 

This can also be recognized by comparing the last-modified times of lh.aparc.stats and lh.pial-files, where the time of the first is older than compared to the latter. Moreover the ?h.aparc.stats of separate freesurfer runs with and without pial surface correction are identical. 

Is this a known issue? 

Best,

Martijn