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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