Can you check if these 2 processes are still around using 'ps -p 2398610 2398617'?

It looks like your recon-all is started with '-parallel' option. It is the multi-processing done at the recon-all level. There is no synchronization mechanism to ensure shared resources access/update. Use '-nthreads N' to enable multithreading at each program level.

Yujing

From: Sambamoorthy, Sowmya Sowmya.Sambamoorthy@UTDallas.edu Sent: Tuesday, September 30, 2025 5:35 PM To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Cc: Kidwai, Ambereen Amber.Kidwai@utdallas.edu Subject: [Freesurfer] Waiting for PID error.

External Email - Use Caution Dear Experts,

One of my recon-all seems to be in a hung state. Started the recon at 10AM and its still going on - we have other brains that typically finish within 4 hrs.

These are the last few entries from the recon-all log. Should I kill this process? What could be the root cause for this state?

Any help appreciated. TIA!

-Sowmya

280/300: dt: 0.9000, rms radial error=124.996, avgs=0 285/300: dt: 0.9000, rms radial error=124.336, avgs=0 290/300: dt: 0.9000, rms radial error=123.681, avgs=0 295/300: dt: 0.9000, rms radial error=123.030, avgs=0 300/300: dt: 0.9000, rms radial error=122.383, avgs=0

spherical inflation complete. epoch 1 (K=10.0), pass 1, starting sse = 152036.29 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.01/13 = 0.00112 epoch 2 (K=40.0), pass 1, starting sse = 54086.27 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.05/13 = 0.00388 epoch 3 (K=160.0), pass 1, starting sse = 32919.19 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.09/14 = 0.00615 epoch 4 (K=640.0), pass 1, starting sse = 27218.02 taking momentum steps... taking momentum steps... taking momentum steps... taking momentum steps... pass 1 complete, delta sse/iter = 0.11/15 = 0.00710 final distance error %100000.00 writing spherical brain to ../surf/rh.qsphere.nofix spherical transformation took 0.1488 hours FSRUNTIME@ mris_sphere 0.1488 hours 4 threads #VMPC# mris_sphere VmPeak 2099556 mris_sphere done PIDs (2329613 2329616) completed and logs appended. #@# Fix Topology lh Tue Sep 30 11:59:56 CDT 2025

mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 lh

#@# Fix Topology rh Tue Sep 30 11:59:56 CDT 2025

mris_fix_topology -mgz -sphere qsphere.nofix -inflated inflated.nofix -orig orig.nofix -out orig.premesh -ga -seed 1234 fmri102_114 rh

Waiting for PID 2398610 of (2398610 2398617) to complete...