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