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Hello FreeSurfer developers,
I would like to report a possible bug in recon-all / expert options handling in FreeSurfer 8.1.0.
Environment
- FreeSurfer version: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed - OS: Ubuntu 22.04, Linux 6.8.0-107-generic x86_64
What I am trying to do I am running recon-all on a hi-res dataset and want to increase the number of inflation iterations using an expert options file.
expert.opts content mris_inflate -n 100
Command export SUBJECTS_DIR=/mnt/data4/test
recon-all -all -subjid sub-01 -i /mnt/data4/Subjects/T1_MPR.nii -T2 /mnt/data4/Subjects/T2_SPC.nii -T2pial -hires -expert /home/kami/expert.opts -xopts-overwrite -openmp 8
Observed behavior The subject-specific scripts/expert-options file is created correctly and contains: mris_inflate -n 100
However, when recon-all reaches Inflation1, the executed command in recon-all.log becomes:
mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
So the "-n" appears to be dropped, and "100" is interpreted as an input surface filename. The run then fails with:
Reading 100 ** failed to open GIFTI XML file '100.gii' mrisReadGIFTIdanum: ERROR reading gifti 100.gii [INFO] read, cannot find 100, trying 100.gii ... error: No such file or directory error: mris_inflate: could not read surface file 100
Relevant log excerpt #@# Inflation1 lh Fri Apr 10 07:16:38 PM JST 2026 /mnt/data4/test/sub-01/scripts
mris_inflate -no-save-sulc 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 100 ** failed to open GIFTI XML file '100.gii' mrisReadGIFTIdanum: ERROR reading gifti 100.gii [INFO] read, cannot find 100, trying 100.gii ... error: No such file or directory error: mris_inflate: could not read surface file 100
What I expected I expected recon-all to execute:
mris_inflate -no-save-sulc -n 100 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Additional notes
- The expert options file itself is plain text with normal LF line ending. - cat -A /home/kami/expert.opts shows: mris_inflate -n 100$ - od -c /home/kami/expert.opts shows: 0000000 m r i s _ i n f l a t e - n 0000020 1 0 0 \n - mris_inflate itself appears to work normally when run directly. - I also tried -xopts-overwrite, but the same issue occurs.
This looks like a recon-all expert-options parsing / argument-passing problem, where the "-n" option is lost before invoking mris_inflate.
Please let me know if you would like the full recon-all.log and recon-all.cmd attached. I can also provide a minimal reproducible example.
Best regards,Toshiharu
---------------------------------------------------------------------------------------------------- Toshiharu Kamishikiryo M.D.,Ph.D. Department of Psychiatry and Neurosciences. Graduate School of Biomedical & Health Sciences, Hiroshima University. -----------------------------------------------------------------------------------------------------