The 'mris_inflate' doesn't seem to be constructed correctly.
The recon-all was run with expect options. /usr/local/freesurfer/8.1.0/bin/recon-all -i /mnt/hpcdata/TANDEM/FSL_SIENAX/sub-9203_ses-01/struct_bias_head.nii.gz -all -hires -expert /mnt/hpcdata/TANDEM/FS_DIR/expert.opts -subjid sub-9203_ses-01
What are the additional options in your /mnt/hpcdata/TANDEM/FS_DIR/expert.opts?
Yujing
From: Su, Weizhong wayne.su@ubc.ca Sent: Monday, August 18, 2025 4:01 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Freesurfer 8.1.0 failed with hires opton
External Email - Use Caution Hello FreeSurfer Developers,
I'm attempting to use Freesurfer v8.1.0 with -hires option (mris_inflate -n 50), but I get the following error when I run the recon-all command:
mris_inflate -no-save-sulc 50 ../surf/lh.smoothwm.nofix ../surf/lh.inflated.nofix
Not saving sulc Reading 50 ** failed to open GIFTI XML file '50.gii' mrisReadGIFTIdanum: ERROR reading gifti 50.gii [INFO] read, cannot find 50, trying 50.gii ... error: No such file or directory error: mris_inflate: could not read surface file 50\00 Command exited with non-zero status 255
I have tired recon-all without -hires option, and FS finished without any error. Does anyone have any thoughts on how to trouble-shoot this one?
1) FreeSurfer version: freesurfer_ubuntu22-8.1.0_amd64.deb 2) Platform: Ubuntu V22.0.4 3) uname -a: Linux hpc11 5.15.0-105-generic #115-Ubuntu SMP Mon Apr 15 09:52:04 UTC 2024 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached
Another question regarding Freesurfer v8: Is it still good to use T2 for pial surface refinement since FS v8 has used machine learning approach already?
Thanks, Wayne