Hello all,
My site has recently upgraded to the newest version of Freesurfer, and I've run a set of subjects on recon-all using the hippocampal subfield segmentation flag. Everything went well. Then in running kvlQuantifyHippocampalSubfieldSegmentations.sh, I received error messages indicating that certain expected files didn't exist.
In particular, among output files labeled with the scheme $subj/mri/posterior_$side_$struct.mgz, the script expected ...CA2-3.mgz and ...CA4-DG.mgz, and existing files were named ...CA2_3.mgz and ...CA4_DG.mgz -- in other words, the script expected a hyphen but instead the filenames contained an underscroe.
After renaming the files appropriately, kvlQuantify... successfully generated the nonPartialVolumeStats files and everything worked fine.
I didn't see any threads with this solution, and only one or two that mentioned the problem (http://bit.ly/1vHbV5K), so I thought I'd offer it up in case it could be addressed in a future release.
Cheers, C.P. Frost