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
