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>:
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
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
To unsubscribe send an email to freesurfer-leave@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman3/lists/freesurfer@nmr.mgh.harvard.edu/
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 at https://www.massgeneralbrigham.org/complianceline <https://www.massgeneralbrigham.org/complianceline> .
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.