External Email - Use Caution
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://secure-web.cisco.com/1S-XRYZwdfIh6LBaYDmryClXzVhMGn3s7IZR6N9Pa3Ony7_a... ```
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 * Checked for any outdated `license.txt` in `$FREESURFER_HOME` and replaced it.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