Hi Christopher,

I noticed that you were only running ‘recon-all -autorecon1 -autorecon2’. I don’t think ?h.white surface are generated for the command combinations. ‘recon-all -all’ will run all recon steps and generate ?h.white.

Here is a description of recon-all process and flags:

https://surfer.nmr.mgh.harvard.edu/fswiki/recon-all

Best,

Yujing

From: freesurfer-bounces@nmr.mgh.harvard.edu <freesurfer-bounces@nmr.mgh.harvard.edu> On Behalf Of Christopher Mcnorgan
Sent: Wednesday, November 23, 2022 5:10 PM
To: freesurfer@nmr.mgh.harvard.edu
Subject: [Freesurfer] recon-all failing to generate wm surface

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A student and I have independently been trying to reconstruct a dataset. We've tried it a couple different ways using either an additional FLAIR or a T2 image and always hit a point where the process halts because of a missing surface file:

Loading lh.white surf

error: No such file or directory

error: MRISread(/home/cpmcnorg/VMP/FS_002/surf/lh.white): could not open file

This has happened when running just the autorecon1 step or both autorecon1 and autorecon2. I'm using freesurfer 7.2.0 on a linux computer, and my student is running 7.3.2 on a Mac. In my most recent test, I ran

recon-all -autorecon1 -autorecon2 -i <path to T1 file> -T2 <path to T2 file> -subjid <ID>

and I have several surface files (e.g., ?h.orig and even ?h.white.preaparc) but not the ?h.white surface. I'm unclear what's causing the recon-all script to look for the wm surface before it's been created.