FreeSurfer

• Analyses with qdec
• FreeSurfer Processing Steps
• Results - extracting values
• Tracula
• Troubleshooting
• Updating Freesurfer
• View subject processing
• Viewing Pial Surface and Correcting Errors in FreeSurfer

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
doug

Create 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