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Hello FreeSurfer Team,
What I am trying to accomplish: I am running a full recon-all (-all) and trying to control the number of inflation iterations via an expert options file containing: "mris_inflate -n 30"
FreeSurfer version and platform: freesurfer-linux-ubuntu22_x86_64-8.1.0-20250719-f30dfed Running inside Docker based on Ubuntu 22.04
Command I ran: recon-all -i /data/test/sub-0113_t1_axisAlign.nii.gz -s sub-0113 -all -hires -parallel -openmp 16 -expert /data/test/expert_inflate30.opts
Error/output seen: During the Inflation1 stage, the log shows mris_inflate being invoked without the -n flag and with a bare "30" argument: mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix Shortly after, recon-all exits with ERRORS.
The recon-all.log file have these lines at the end:
#@# Inflation1 lh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts
mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
#----------------------------------- #@# Inflation1 rh Thu Sep 4 13:54:46 UTC 2025 /data/subjects/sub-0113/scripts
mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
Waiting for PID 4083 of (4083 4086) to complete... Waiting for PID 4086 of (4083 4086) to complete...
mris_inflate -no-save-sulc 30 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30
mris_inflate -no-save-sulc 30 ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix
Not saving sulc Reading 30 ** failed to open GIFTI XML file '30.gii' mrisReadGIFTIdanum: ERROR reading gifti 30.gii [INFO] read, cannot find 30, trying 30.gii ... error: No such file or directory error: mris_inflate: could not read surface file 30 PIDs (4083 4086) completed and logs appended. Linux 4fa29909686b 6.8.0-78-generic #78-Ubuntu SMP PREEMPT_DYNAMIC Tue Aug 12 11:34:18 UTC 2025 x86_64 x86_64 x86_64 GNU/Linux recon-all -s sub-0113 exited with ERRORS at Thu Sep 4 13:54:46 UTC 2025
Troubleshooting already tried: - Recreated the expert file to ensure ASCII hyphen and LF newline: printf 'mris_inflate -n 30\n' > /data/test/expert_inflate30.opts - Resumed with overwrite -xopts-overwrite -expert /data/test/expert_inflate30.opts - Verified that mris_inflate accepts -n 30 manually:: /usr/local/freesurfer/8.1.0/bin/mris_inflate -no-save-sulc -n 30 in.surf out.surf - Other expert options (e.g., "mris_smooth -seed 9999") are honored and appear correctly in the log
Is there a known issue in FreeSurfer 8.1.0 on Ubuntu 22.04 where expert options for mris_inflate are not applied? What is the recommended way to ensure -n 30 is honored?
Thank you for your help.
Best regards, Yahia Mokli