Problem with running FreeSurfer


I am trying to run some tests using FreeSurfer 6.0.

The analysis seems to be running fine at the beginning and then exits with the following error “nu_correct: Command not found.
ERROR: nu_correct”. When I searched this error online it is most likely connected to the fact that FreeSurfer cannot get access to specific file because the path to a folder MNI_DIR is not correct. I put this folder in my scratch area and sourced it but I keep getting the same error.

If you want to look at the full log of the run you can find it here


I would appreciate any input about running FreeSurfer on Baobab

Best regards

Dear Federica,

This version on Baobab seems to be completely broken as almost no env variable related to FreeSurfer are set, weird.

I installed version 6.0.1 and the env variables seems to be set correctly.

Please give a try:

ml FreeSurfer/6.0.1-centos6_x86_64


edit: the version 6.0.0 on Baobab was compiled 3 years ago!