The issue disappeared after enclosing the expert option with double quotes in expert.opts file:

"mris_inflate -n 30"

But it is unclear if this effort solved this problem because the recon-all.log does not show use of -n 30:

mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

mris_inflate -no-save-sulc ../surf/rh.smoothwm.nofix ../surf/rh.inflated.nofix

mris_inflate -no-save-sulc ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix

...

mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated

mris_inflate ../surf/rh.smoothwm ../surf/rh.inflated

mris_inflate ../surf/lh.smoothwm ../surf/lh.inflated

...

@Douglas N. Greve, can you comment?

Best,
Tashrif

From: Mokli, Yahia <yahia.mokli@psychiat.med.uni-giessen.de>
Sent: Tuesday, November 11, 2025 7:12 AM
To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu>; Billah, Tashrif <tbillah@bwh.harvard.edu>
Subject: Re: [Freesurfer] expert.opts is not parsed correctly in FS 8

External Email - Use Caution

Dear Tashrif,

I ran into the same issue and got a fix from Douglas N. Greve in late September (a new fsr-getxopts script) as noted in the attached email. I was told to copy it to $FREESURFER/bin and make it executable.

Best,

Yahia

Am 11.11.2025 um 04:20 schrieb Billah, Tashrif <tbillah@bwh.harvard.edu>:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all#ExpertPreferences-1

Did you guys change how parameters from expert.opts is ingested by recon-all in FS 8.1.0? We have successfully been using the following line in expert.opts file with FS 7:

mris_inflate -n 30

(https://surfer.nmr.mgh.harvard.edu/fswiki/mris_inflate)

But now, FS 8.1.0 recon-all gives an error:

```

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

```

This almost certainly means FS 8.1.0 is not parsing expert.opts line correctly. The "-n 30" is bein parsed as just "30".

Best,
Tashrif

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