Following your advice below, it was clearly apparent that the output from the skull stripping step was missing a lot. I tried adjusting the -wsthresh flag from 50 -> 200 and it still left major parts of the brain out.

I have a good quality mri and subject with no known anatomical abnormalities.

The log file indicates "surface validation has detected possible Error"

Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing?

Log file attached.

Thanks,

-Matt

Bruce Fischl Fri, 02 Mar 2018 08:00:11 -0800

Hi Matt

check the output of the skull stripping. This error usually means that too much (everything?) has been erased and no plausible cc could be found

cheers

Bruce

On Thu, 1 Mar 2018, Matthew Grecsek wrote:

My recon-all ended prematurely with the following message:

final transformation (x=136.0, yr=-10.054, zr=-0.114):

0.98464 0.00200 -0.17457 15.51372;

-0.00197 1.00000 0.00035 17.22442;

0.17457 0.00000 0.98464 -17.83761;

0.00000 0.00000 0.00000 1.00000;

mri_cc: no WM voxels found with norm > 40 -- check skull stripping

No such file or directory

Linux centos-7-1 3.10.0-693.17.1.el7.x86_64 #1 SMP Thu Jan 25 20:13:58 UTC 2018

x86_64 x86_64 x86_64 GNU/Linux

recon-all -s matt2 exited with ERRORS at Thu Mar 1 04:35:09 UTC 2018

I am running: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

My full log file is attached.

Please let me know suggestions for correcting and continuing the process.

Thanks,

-Matt

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