Problem with running FreeSurfer

HPC Technical
1

Hello!

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

/home/users/r/ribaldi9/scratch/jobs/stdout_1.txt

I would appreciate any input about running FreeSurfer on Baobab

Best regards

2

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

Best

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