Hi FreeSurfer community,

 

I'm running into an issue with the longitudinal FreeSurfer pipeline.

 

Background:

 

I'm working with T1-weighted MRI scans from an aerobic exercise intervention study in older adults (age 60+).

I have two timepoints per subject: pre- and post-intervention.

Cross-sectional `recon-all` has successfully completed for both timepoints.

I'm now trying to run the longitudinal pipeline using `recon-all -base`, but I'm getting a glibc/license-related error.

 

Command:

 

```bash

recon-all -base sub002base \

  -tp /rds/projects/s/segaertk-chbh-00077/Structural/FreeSurfer/sub002_tp1 \

  -tp /rds/projects/s/segaertk-chbh-00077/Structural/FreeSurfer/sub002_tp2 \

  -all

```

 

Error:

```

GNU libc version: 2.28

ERROR: Systems running GNU glibc version greater than 2.15

  require a newly formatted license file (it's free). Please

  download a new one from the following page:

  http://surfer.nmr.mgh.harvard.edu/registration.html

```

 

Notes:

 

I have a valid, updated license file (downloaded from the official site).

I set the license path before running the command:

 

  ```bash

  export FS_LICENSE=${HOME}/license.txt

  ```

Weirdly, the cross-sectional `recon-all` works fine using the same environment and license file.

 

I'm using FreeSurfer version: FreeSurfer/6.0.1-centos6_x86_64

My system is running glibc 2.28.

 

What I've Tried:

 

• Verified that `$FS_LICENSE` is exported and correct.
• Checked for any outdated `license.txt` in `$FREESURFER_HOME` and replaced it.
• Confirmed that `recon-all -version` and `which recon-all` return the expected FreeSurfer install.
• Deleted partial `sub002base` folder and retried clean.

 

Has anyone encountered this behaviour — where the cross-sectional `recon-all` works, but `recon-all -base` fails due to the license/glibc issue?

 

Any help would be greatly appreciated!

 

Warmest regards,

Foyzul.

 

Dr Foyzul Rahman

Centre for Human Brain Health (CHBH)

University of Birmingham

United Kingdom