Hallo,
I have finished my test runs and have observed that using export
DIAG=0x and export DIAG_VERBOSE=1 cause all recon-all runs to fail with
the following error:
HIPS unsupported
No such file or directory
I have tested different computing environments (container, hardware, VMs) using
itioned to open source ages ago as their
license wasn't compatible
On Wed, 31 May 2017, Jens Offenbach
wrote:
> Hallo,
> first of all: Sorry to be a little bit clingy, but I have some problems in
> understanding regarding the DIAG option in FreeSurfer. As suggested by Bruce,
> I
Hallo,
first of all: Sorry to be a little bit clingy, but I have some problems in
understanding regarding the DIAG option in FreeSurfer. As suggested by Bruce, I
have set DIAG to 0x and DIAG_VERBOSE to 1. I am getting a lot of output
now and a very large recon-all.log.
Unfortunately, I
support list"
Betreff: Re: [Freesurfer] Segmentation fault (core dumped) error
hmmm, if you tar and gzip that subject and upload it to our ftp site we
will see if we can replicate the problem
On Mon, 29 May 2017, Jens Offenbach
wrote:
> This says the system's log:
>
> May 29
c0 ip 7f3509aa0194 sp 7ffeee7af590 error 4 in
libc-2.23.so[7f3509a53000+1bf000]
There are two more runs shortly before the problematic section. I will report,
if the issue appears there, too.
Regards,
Jens
Gesendet: Montag, 29. Mai 2017 um 07:41 Uhr
Von: "Jens Offenbach"
I am facing a similar issue with recon-all in FreeSurfer 6.0.0. on two subjects
from OASIS-Brains.
I will retry the run.
This is the last log entry:
mri_cc -aseg aseg.auto_noCCseg.mgz -o aseg.auto.mgz -lta
/home/ubuntu/freesurfer/subjects/OAS1_0004_MR1/mri/transforms/cc_up.lta
OAS1_0004_MR1
e
out lots of things though
On Wed, 24 May 2017, Jens Offenbach wrote:
> Hallo,
> I must run FreeSurfer 6.0.0 with a maximum level of verbosity. I require as
> much log output as possible for monitoring purposes. Someone gave me the hint
> to run recon-all with DIAG=0x04040.
Hallo,
I must run FreeSurfer 6.0.0 with a maximum level of verbosity. I require as
much log output as possible for monitoring purposes. Someone gave me the hint
to run recon-all with DIAG=0x04040. Is this the highest possible log level for
running FreeSurfer.
Thank you very much.
Regards,
Jens
than the directory being touched). this could be something
the program missed, or is actually true.
cheers,
satra
On Wed, Nov 19, 2014 at 5:03 PM, Jens Offenbach
wrote:Hi satra,
I have tried to find some posts about the minimum files required to run
recon-all, but I cannot find anything
e to create it: http://www.pgbovine.net/cde.html
this reduces the archive down to about 650MB comprising binaries and atlases.
this wouldn't be for general purpose freesurfer processing, just for running
recon-all.
cheers,
satra
On Wed, Nov 19, 2014 at 8:40 AM, Jens Offenbach
wrote:I
nt of Neurological Surgery
University of Pittsburgh
(412)648-9654 Office
(412)521-4431 Cell/Text
> -Original Message-
> From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-
> boun...@nmr.mgh.harvard.edu] On Behalf Of Jens Offenbach
> Sent: Wednesday, November 19,
We are currently working on a solution that brings FreeSurfer in the cloud.
Unfortunately, we are facing a lot of problems. Hopefully, someone can help me:
I want to run FreeSurfer on Ubuntu 14.04 or 14.10. What package is required to
download (CentOS 4 x86_64 (64b))? Does it work anyway on the
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