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
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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-1https://secure-web.cisco.com/1QXmU13Mu415p1WiYq-vg4D_9Mrj3ZoPGlO7aBkkTW7DMzGsSzr8te-3SySDpyt6A7w8ztV10CV3xL8PHY3nbuHKTRT0WB0pG-Vh8q_vDMyIqjwlp8IVc64Uat4sv1_lSnO0fGaBgSm6Xq1pZsPZ8Y8_N1VQn87e-MmPk1IoPgHxzB5TVzgE5Jw74dENwyxcyhZOsG1i1IN4yA3nI0V1L6IskzA31626muq5N1MOIk8XN_fkX6p_BiNaxz07Bpti-fFpqg7HArhLM-QSIpOIbSu9Yb6gEck30dbJXAHWb-XBttHMaW4zlY1NvCHKIvAklRe239SObR6u76lNuodrKyQ/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Frecon-all%23ExpertPreferences-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_inflatehttps://secure-web.cisco.com/1kLptWT2kmcz0pnfwJ-aWcGmYvD7SXbeH5SNvdnuuM_bOQGolFViKvgEs0pC35akvI2ny_kt1ISKAxMV9nbIi39TIZhCWvgaW5AFTXeIQ_Y1iJ_VoVFgcpNu3qsYo4N6FV9qm4Xid68on1NpHYbQkLOYmOR_VH3ky7hRopS4-56UQyngL60RNILafmNVuS06ImWvHDVHZKlHU_CXJuayQc80aO0Rms5B_Rrp8nFfHtTiFFc9TN8iKvQ_eWbgyykAyXMYMKSPfwxGFqoQmBMxnvvtqEtNBxQPRVyADCKnNcLLygdxDYEz5E5TsWPG07PgX2NaF8AMl6QCYXOBZHlZHOg/https%3A%2F%2Fsurfer.nmr.mgh.harvard.edu%2Ffswiki%2Fmris_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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