Hi Bruce,

My apologies, I had forgotten that we had set FREESURFER_HOME up in our pipelines separately, and had I just got the version off of my shell.

We are using freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c

Should I upload the subject somewhere?

Thanks,

Trevor

From: Bruce Fischl
Sent: Thursday, December 14, 2017 7:06 AM
To: Freesurfer support list
Subject: Re: [Freesurfer] White/pial surface failure

Hi Trevor

would you consider moving to V6? The high res stream is *much* better in
it than 5.3. If you can't, upload the subject and we will take a look

cheers
Bruce


On Thu, 14 Dec 2017, Trevor K Day wrote:

>
> Hello,
>
>  
>
> We are trying to run the high-resolution pipeline and it has failed spectacularly on one of our
> subjects.
>
> Two images from recon_checker are attached.
>
>  
>
> I’m stumped because the command exits with an exit code of 0 and, in looking at the log, there no
> obvious indication of any error.
>
> I’m not sure what to search because I don’t have an error message.
>
> Recon-all.log is attached.
>
>  
>
> The brainmask is fine. Not perfect, but certainly not poor enough to cause this.
>
> The intensity values of the T1 are perfectly normal, and there’s a bit of a motion artifact in the
> frontal lobe, but nothing that freesurfer hasn’t handled before.
>
>  
>
> Others have suggested that this seems to extreme to fix with control points, are the other
> approaches to take?
>
>  
>
> The command used was:
>
>  
>
> /usr/local/freesurfer/stable6_0/bin/recon-all \
>
>                 -all -s 170661.s1 -hires -cw256 -qcache \
>
>                 -i /mnt/panuc/udallp2/subjects/170661/session1/mprage/T1_256.nii.gz \
>
>                 -expert /mnt/panuc/udallp2/lib/expert.opts
>
>  
>
> (Again, T1_256.nii.gz looks totally fine.)
>
>  
>
> The contents of expert.opts are mris_inflate -n 30
>
>  
>
>  *  Freesurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0
>  *  Platform: Debian GNU/Linux 8.9 (jessie)
>  *  Uname -a: Linux panuc 3.16.0-4-amd64 #1 SMP Debian 3.16.43-2+deb8u5 (2017-09-19) x86_64
>     GNU/Linux
>
>  
>
> Where can I start to debug and fix this?
>
>  
>
> Thanks,
>
> Trevor Day
>
>
>