External Email - Use Caution Hello Pei-Ying, It does not work to run freesurfer/recon-all command(s) on subject data that lives on a Windows formatted drive (in your case visible from inside the Linux VM via the mount point to drive d, /mnt/d). The SUBJECTS_DIR needs to point to a path in the VM Linux filesystem since Windows file systems, e.g., NTFS, do not support symbolic linking of files. One way to do that is to put your subject data under your home directory in the Linux VM. $ cd $HOME$ mkdir subject_data… copy in your data to process from /mnt/d …… setup the freesurfer environment as usual by setting FREESURFER_HOME and source the shell init file …… then change SUBJECTS_DIR to point the new location in your Linux $HOME directory ...$ export SUBJECTS_DIR=$HOME/subject_data - R.
On Jan 1, 2025, at 22:17, 蔡佩穎 <pcai...@gmail.com> wrote: External Email - Use Caution Dear FreeSurfer Team, I am attempting to run Recon-all on my data from my research institute, using WSL Ubuntu22.04.5 LTS. On my first attempt to run Recon-all, I got the error shown below: #@# Curv .H and .K rh Thu Jan 2 00:06:17 CST 2025 /mnt/d/suicide/Raw_UD/UD001/surf mris_curvature -w -seed 1234 rh.white.preaparc rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated cd /mnt/d/suicide/Raw_UD/UD001/surf reconbatchjobs /mnt/d/suicide/Raw_UD/UD001/scripts/recon-all.log mris_curvature_white_lh.cmd rm_curvature_white_lh.H.cmd ln_curvature_white_lh.H.cmd rm_curvature_white_lh.K.cmd ln_curvature_white_lh.K.cmd mris_curvature_inflated_lh.cmd mris_curvature_white_rh.cmd rm_curvature_white_rh.H.cmd ln_curvature_white_rh.H.cmd rm_curvature_white_rh.K.cmd ln_curvature_white_rh.K.cmd mris_curvature_inflated_rh.cmd Waiting for PID 5816 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5819 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5822 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5825 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5828 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5831 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete.... Waiting for PID 5834 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5837 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5840 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5843 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5846 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... Waiting for PID 5849 of (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) to complete... mris_curvature -w -seed 1234 lh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 12.423*4pi (156.109) --> -11 handles ICI = 177.4, FI = 1660.9, variation=26709.915 writing Gaussian curvature to ./lh.white.preaparc.K...done. writing mean curvature to ./lh.white.preaparc.H...mris_curvature done. rm -f lh.white.H ln -s lh.white.preaparc.H lh.white.H ln: failed to create symbolic link 'lh.white.H': Operation not permitted rm -f lh.white.K ln -s lh.white.preaparc.K lh.white.K ln: failed to create symbolic link 'lh..white.K': Operation not permitted mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 lh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 154 vertices thresholded to be in k1 ~ [-0.54 0.37], k2 ~ [-0.15 0.16] total integrated curvature = 0.361*4pi (4.532) --> 1 handles ICI = 1.5, FI = 8.8, variation=154.684 133 vertices thresholded to be in [-0.04 0.03] writing Gaussian curvature to ./lh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 133 vertices thresholded to be in [-0.22 0.14] done. writing mean curvature to ./lh.inflated.H...curvature mean = -0.016, std = 0.023 mris_curvature done. mris_curvature -w -seed 1234 rh.white.preaparc setting seed for random number generator to 1234 total integrated curvature = 23.152*4pi (290.942) --> -22 handles ICI = 182.8, FI = 1734.3, variation=27614.160 writing Gaussian curvature to ./rh.white.preaparc.K...done. writing mean curvature to ./rh.white.preaparc.H...mris_curvature done. rm -f rh.white.H ln -s rh.white.preaparc.H rh.white.H ln: failed to create symbolic link 'rh.white.H': Operation not permitted rm -f rh.white.K ln -s rh.white.preaparc.K rh.white.K ln: failed to create symbolic link 'rh.white.K': Operation not permitted mris_curvature -seed 1234 -thresh .999 -n -a 5 -w -distances 10 10 rh.inflated setting seed for random number generator to 1234 normalizing curvature values. averaging curvature patterns 5 times. sampling 10 neighbors out to a distance of 10 mm 157 vertices thresholded to be in k1 ~ [-0.46 0.97], k2 ~ [-0.22 0.16] total integrated curvature = 0.314*4pi (3.949) --> 1 handles ICI = 1.4, FI = 9.6, variation=164.776 152 vertices thresholded to be in [-0.07 0.03] writing Gaussian curvature to ./rh.inflated.K...thresholding curvature at 99.90% level curvature mean = 0.000, std = 0.002 107 vertices thresholded to be in [-0.21 0.22] done. writing mean curvature to ./rh.inflated.H...curvature mean = -0.017, std = 0.024 mris_curvature done. PIDs (5816 5819 5822 5825 5828 5831 5834 5837 5840 5843 5846 5849) completed and logs appended. Linux DESKTOP-M947IPI 5.15.167.4-microsoft-standard-WSL2 #1 SMP Tue Nov 5 00:21:55 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux recon-all -s UD001 exited with ERRORS at Thu Jan 2 00:06:41 CST 2025 I tried following one of the suggestions in the archives: Method one /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 root root 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects udo chown -R bml-4090:bml-4090 /usr/local/freesurfer/7.4.1/subjects ls -ld /usr/local/freesurfer/7.4.1/subjects drwxr-xr-x 14 bml-4090 bml-4090 4096 Dec 31 16:45 /usr/local/freesurfer/7.4.1/subjects Method two bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:03 lh.white.H -> lh.white.preaparc.Hbml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.H lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 rh.white.H -> rh.white.preaparc.H bml-4090@DESKTOP-M947IPI:~$ ls -l rh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 rh.white.K -> rh.white.preaparc.K bml-4090@DESKTOP-M947IPI:~$ ls -l lh.white.K lrwxrwxrwx 1 bml-4090 bml-4090 19 Jan 1 21:02 lh.white.K -> lh.white.preaparc.K How can I allow symbolic links? Thank you so much for your help!Happy new year! Best wishes, Pei-Ying <recon-all.log>
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