I have found and fixed this bug. I've attached a new version of the fsr-getxopts script. You can copy it into $FREESURFER/bin Change the permissions to make it executable chmod a+x $FREESURFER/bin/fsr-getxopts

On 9/4/2025 1:29 PM, Su, Weizhong wrote:

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Hi Yahia,

I faced same issue when using mris_inflate expert option. Do not use this option for Freesurfer v8.1.0 until FS developer team fixes this problem.

Best,

Wayne

*From: *"Mokli, Yahia" yahia.mokli@psychiat.med.uni-giessen.de *Reply-To: *Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Date: *Thursday, September 4, 2025 at 8:53 AM *To: *"freesurfer@nmr.mgh.harvard.edu" freesurfer@nmr.mgh.harvard.edu *Subject: *[Freesurfer] recon-all: expert options not applied to mris_inflate

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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

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