You can also do this This is a known error where it is filtering out the "-n" flag, and that causes an error. To get around it, you can download the current dev version and copy cp $DEV/bin/fsr-getxopts $FREESURFER/bin/fsr-getxopts that should fix it
On 11/18/2025 4:16 PM, Billah, Tashrif wrote:
After further investigation, I see that enclosing the expert option with double quotes did not apply the "-n 30".
@Douglas Greve, the file you sent to Yahia, did you only enclose $tmp[2-$#tmp] with double quotes in line 76 compared to what you packaged with FS 8.0?
Best, Tashrif
*From:* Billah, Tashrif tbillah@bwh.harvard.edu *Sent:* Tuesday, November 11, 2025 10:04 AM *To:* Freesurfer support list freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] expert.opts is not parsed correctly in FS 8 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 <https://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_inflate <https://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 _______________________________________________ Freesurfer mailing list --freesurfer@nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> To unsubscribe send an email tofreesurfer-leave@nmr.mgh.harvard.edu <mailto:freesurfer-leave@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/ <https://secure-web.cisco.com/1k9jGQJvTHPAyyvEyK2lcF6YbR6MdXMPyCRHTTfb8LlSteo81khfBm2ylOr6J8hAiqbczWcEXif1i5wgDjKNY1XDYuTBZ_rwbBVQqHuP3O4eVlZOEKpGWivaapg0znoMIHb4Q-I5YhSdh8AdfOoBLJF7QEPccofVV5cHNYBQA_Lba1GJiAXz2EqCKe42Fmq2pnHfqvm8KFZiYitnP1Q8a5UtxBp0Huj7Z7PMDWLBlC-GNxKnUVhWKh_KfzU1MCw1OzmLotg9kqz_4Hme4wrPPJ1IXl4XVTOsf01BxdMuzZkwQ4AwtU4bhPsubzZ0CcI_0x401sogsXKNrsRLFIdnRqA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman3%2Flists%2Ffreesurfer%40nmr.mgh.harvard.edu%2F> The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Mass General Brigham Compliance HelpLine athttps://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1K1xcVY42GzPw9ZmyY9iQWne4Yy0EO6wToRQiVj2fhpddwFVLucR5aK4JB-XxQ086wfo-qIFts9vABagwPIfg1y6uNCMtrX85WuHmT88tnLiU9YjvqMuqEip_UeFrV7iAy28nB41Y1EZaJPuP334UFfHG_oK3DDlT9BHALC8L1-8cYmWd51QBMKyD2zjFfBJXP0BsO48YKeWIwzBb7OefeZCvEins5oZu0fjdrW8p2kyu68IsGPS05coB3fBOpadTF58jhXez7tMD9HJFLsPV7sQ5eADehybBz52U-pFD8TNqgNlSREA03CP4Uy8I0Jlis2V4MP2KKZ9XmoUiUHjk1A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline><https://www.massgeneralbrigham.org/complianceline <https://secure-web.cisco.com/1K1xcVY42GzPw9ZmyY9iQWne4Yy0EO6wToRQiVj2fhpddwFVLucR5aK4JB-XxQ086wfo-qIFts9vABagwPIfg1y6uNCMtrX85WuHmT88tnLiU9YjvqMuqEip_UeFrV7iAy28nB41Y1EZaJPuP334UFfHG_oK3DDlT9BHALC8L1-8cYmWd51QBMKyD2zjFfBJXP0BsO48YKeWIwzBb7OefeZCvEins5oZu0fjdrW8p2kyu68IsGPS05coB3fBOpadTF58jhXez7tMD9HJFLsPV7sQ5eADehybBz52U-pFD8TNqgNlSREA03CP4Uy8I0Jlis2V4MP2KKZ9XmoUiUHjk1A/https%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline>> . Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
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