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Dear FreeSurfer Developers,
I'm attempting to use the recon-all command to reconstruct my participants’ T1w image. However, for my first subject I got the ERROR message as shown below, highlighted in yellow text
SynthStrip: Skull-Stripping for Any Brain Image A Hoopes, JS Mora, AV Dalca, B Fischl, M Hoffmann NeuroImage 206 (2022), 119474 https://secure-web.cisco.com/10_kcPN3k0kfptURbnOBpXPLalN06CN9jiSyVxZ_4dUhl9T... Website: https://secure-web.cisco.com/1O4alEhXXfpduXDK8u0gWl94GE3VCnVsRFU5Pzm78c5SxBw... @#@FSTIME 2026:04:20:15:14:17 mri_synthstrip N 6 e 37.26 S 12.60 U 22.37 P 93% M 5936164 F 1480 R 6260625 W 0 c 73 w 5135 I 394368 O 0 L 0.87 0.56 0.28 @#@FSLOADPOST 2026:04:20:15:14:55 mri_synthstrip N 6 1.01 0.63 0.32 mri_synthseg --i /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/mri/orig.mgz --o /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/mri/synthseg.rca.mgz --threads 1 --vol /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer/sub-02/stats/synthseg.vol.csv --keepgeom --addctab --cpu free(): double free detected in tcache 2 Command terminated by signal 6 @#@FSTIME 2026:04:20:15:14:55 mri_synthseg N 11 e 9.72 S 1.43 U 3.04 P 46% M 456024 F 3608 R 61055 W 0 c 11 w 34031 I 704560 O 8 L 1.01 0.63 0.32 @#@FSLOADPOST 2026:04:20:15:15:04 mri_synthseg N 11 1.17 0.68 0.34 Linux gangoffour 6.6.87.2-microsoft-standard-WSL2 #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-02 exited with ERRORS at Mon Apr 20 15:15:05 BST 2026
I've searched the list and found one same issue on github, however that issue was closed and no answers provided? Also, I’ve attached the recon-all.log for your information .
1) FreeSurfer version: --freesurfer-linux-ubuntu22_x86_64-8.2.0-20260314-d932c45 – 2) My command: -bash: /usr/local/freesurfer/7.3.2/SetUpFreeSurfer.sh: No such file or directory -------- freesurfer-linux-ubuntu22_x86_64-8.2.0-20260314-d932c45 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /usr/local/freesurfer/8.2.0 FSFAST_HOME /usr/local/freesurfer/8.2.0/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /usr/local/freesurfer/8.2.0/subjects MNI_DIR /usr/local/freesurfer/8.2.0/mni FSL_DIR /usr/local/fsl hliu@gangoffour:/mnt/c/Program Files/WSL$ freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ export SUBJECTS_DIR=/mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ echo $SUBJECTS_DIR /mnt/d/repos/CogLearn_fmri-data_formal/fmri/freesurfer hliu@gangoffour:/mnt/c/Program Files/WSL$ cd /mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ ls sub-02_t1w.json sub-02_t1w.nii hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ sudo chmod -R a+w $SUBJECTS_DIR hliu@gangoffour:/mnt/d/repos/CogLearn_fmri-data_formal/fmri/sub-02/anat/1_raw$ recon-all -all -i sub-02_t1w.nii -s sub-02 3) Platform: Windows 11 Enterprise, WSL2, Ubuntu 22 4) uname -a: Linux gangoffour 6.6.87.2-microsoft-standard-WSL2 #1 SMP PREEMPT_DYNAMIC Thu Jun 5 18:30:46 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux 5) recon-all.log: see attached