It looks like you stopped the job and restarted it. Is that correct? If so, I think something might have gotten out of sync. If you did not make any edits (eg, to correct the defects), then can you start it from scratch?

On 5/12/2022 4:29 PM, Margot Wagner wrote:

External Email - Use Caution

Hello FreeSurfer Developers,

I am attempting to run the HCPPipeline using their provided example data according to their Installation and Usage Intructions.

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
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