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
In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
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