Hello FreeSurfer Developers,
Currently, I am trying to run FreeSurferPipelineBatch.sh and got an error message in FreeSurferPipeline.sh when it tries to run mri_surf2surf:
Reading source surface reg /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc
No such file or directory
mri_surf2surf: could not read surface /nadata/cnl/home/mwagner/projects/hcp/Pipelines_ExampleData/100307/T1w/100307/surf/lh.white.preaparc
No such file or directory
ERROR:
This occurs immediately after attempting to run
mri_surf2surf --s 100307 --hemi lh --sval-xyz white.preaparc --surfreg white.preaparc --reg transforms/rawavg2conf.dat rawavg.cmdc.mgz --tval-xyz rawavg.cmdc.mgz --tval white.preaparc.rawavg
It appears no file lh.white.preaparc is made, nor any file matching "white" or "preaparc". I have been unable to find similar errors.
Attached is the output from the FreeSurferPipeline run as well as recon-all.log.
1) FreeSurfer version: freesurfer-x86_64-unknown-linux-gnu-stable6-20170118
2) Platform: Debian GNU/Linux 10 (buster)
3) uname -a: Linux porter 4.19.0-20-amd64 #1 SMP Debian 4.19.235-1 (2022-03-17) x86_64 GNU/Linux
4) recon-all.log: see attached
Thank you for your assistance.
--
Best Regards,
Margot Wagner
Graduate Student Researcher
UCSD Bioengineering