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See also Setting up and running FreeSurfer from CSPM and Display Problems.
Missing files on Analyze ("Couldn't open .../subjects/anat_5020/surf/lh.thickness.fwhm10.fsaverage.mgz")
Several postings on forum (here's one link):
You need to run
recon-all -s subject -qcache
dougCreate a nifti file from FreeSurfer format
In Linux, open a terminal window, go to the directory where the file is stored, and use mri_convert; this will create a copy of the file in the new format (format is determined by extension).
Example - creating a nifti brain mask file for subject CCHS2002:
[...]$ cd /mnt/hgfs/LinuxShare/subjects/CCHS2002/mri
[...]$ mri_convert brainmask.mgz brainmask.nii
Version
cat $FREESURFER_HOME/build-stamp.txt