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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://secure-web.cisco.com/1_lG58AEEMygBXe4mgn79rf73nx9w99E5BM0cU_UhDR05JZ... 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://secure-web.cisco.com/1a-jIWlW7xTqqeE4fl7VtyUXiHuktkI27coSufdTmsqdMIN...)
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".
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