Thanks Doug,
I checked all the limits. This shouldn't be the problem. The descriptor limit is indeed 1024.
I am using
freesurfer-Linux-centos4-stable-pub-v3.0.3
It would be great if you could make the fix available for this version.
Regards,
Stefan
Stephan,
You can find out how many open files are allowed by a process by typing:
limit
and look for the 'descriptors' setting. If that is less than 102, then that is likely your problem, and you could try changing the line to:
limit descriptors 128
If your current descriptors default is some number much greater (like 1024), then the problem is something else.
Which freesurfer distribution are you using? If the problem is indeed the 'too many open descriptors' problem, there was a bug that was fixed to address this (but hasnt yet made to the public distribution), and I could post the binaries for your platform.
Nick
On Thu, 2007-05-03 at 17:26 +0000, skloeppe@uke.uni-hamburg.de wrote:
Hi Doug,
Thanks for your swift reply. When I run your version I always received the error:
"limit: descriptors: Can't remove limit"
I then deleted the following line in your code:
"limit descriptors unlimited "
That helped but after 88 subjects I always get on error message now: "88 of 102: reading
/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz...
mghRead: encountered error executing: 'zcat
/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.
mgz',frame -1 mri_average:
MRIread(/mnt/d/Freesurfer/freesurfer/subjects/average/tmp/make_average_vol-tmp/orig-sMS04797.mgz)
failed"
I am wondering if it might be related to the line I deleted as the one above the deleted one reads
# increase number of allowable open files to maximum:
Many thanks,
Stefan
Copy these into your freesurfer bin
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_surface
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/make_average_subject
then run with --no-link
doug
skloeppe@uke.uni-hamburg.de wrote:
Hi Doug,
I am also running FS on a virtual machine and encoutered the same
problem
with the symbolic links that is described below. When I run the make_average_subject script only data for the right hemisphere is
created.
Then it seems to stop with the message:
ln: creating symbolic link `rh.sphere' to `rh.sphere.reg':
Operation not
supported
I was wondering if you have modified the script to allow a copy
instead of
a link. Will symbolic links be used later in the group analysis steps
as well?
Many thanks,
Stefan
Re: [Freesurfer] symbolic links
Doug Greve Fri, 01 Dec 2006 09:25:04 -0800 I don't think recon-all uses any sym links. I can mod the average subj script to copy instead of link.
[EMAIL PROTECTED] wrote:
Hi Doug,
while trying to expand the volume of my virtual machine to be
able to
create symbolic links I started wondering if the way I preprocessed my data with recon_all might be affected somehow by the fact symbolic
links
were not supported (the data was located on a mounted drive). The only error message regarding this came during the make_average_subject
part...
Is there any way to use freesurfer avoiding the creation of
symbolic
links?
many thanks bogdan
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Phone Number: 617-724-2358 Fax: 617-726-7422
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
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