Hi, Just wanted to follow up on this and see if anyone had a chance to look at it.
Thanks, Trevor Get Outlook for Android<https://aka.ms/ghei36> ________________________________ From: Trevor K Day Sent: Thursday, December 14, 2017 4:09:44 PM To: Freesurfer support list Subject: RE: [Freesurfer] White/pial surface failure Gotcha, uploaded From: Bruce Fischl<mailto:fis...@nmr.mgh.harvard.edu> Sent: Thursday, December 14, 2017 3:39 PM To: Freesurfer support list<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] White/pial surface failure Hi Trevor we need the whole subject dir tarred and gzipped. cheers Bruce On Thu, 14 Dec 2017, Trevor K Day wrote: > > Thanks, uploaded as 170661-T1_256.nii.gz > > > > Trevor > > > > From: Bruce Fischl > Sent: Thursday, December 14, 2017 11:29 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] White/pial surface failure > > > > sure, our ftp site > Bruce > On Thu, 14 Dec 2017, Trevor K Day wrote: > > > > > 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 > > > > > > > > > > > > > > > > > > > > > > > >
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