Hi Jens
you could estimate it, but it might not be exactly right. There's no way to
know how long it will take to converge as it depends on the details of the
anatomy. If the current output is not verbose enough for you, you can turn
on more output by:
setenv DIAG 0x04040
if you run some recons with this on you'll be able to get an idea of how
many integration steps each pipeline step takes
cheers
Bruce
On Wed, 19 Nov 2014, Jens Offenbach wrote:
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 Ubuntu family?
On the FTP server I have found a patch for 5.3.0, but I am not sure how to
apply it or if I must apply it? The Readme says to replace “mri_segstats”. What
about the other files “recon-all, fsfast, tksurferfv, …”?
I want to reduce the archive to its bare minimum, otherwise the automated
deployment process takes too long. It should contain only those files which are
necessary to execute the pipeline without any viewer or examples. Which files
and folders can be deleted safely?
The most important issue is to monitor the FreeSurfer pipeline execution. I
know that the scripts folder contains some status files which offer important
data helping me to monitor the pipeline execution progress of “recon-all”.
Unfortunately, that is not enough… If one step takes e.g. approximately 20
hours, I have to say something about the progress within this current step. Is
there any possibility to monitor the progress of a single step. We need
something that allows us to say e.g. that Step “CA Reg” has 34 % of its work
done so far which means that the overall pipeline progress is e.g. 63 %. Is it
possible to say that a specific step takes a specific portion of the overall
pipeline execution time. What influences this portion (format or quality of
input, platform, …)?
Thank you very much for your help!
Regards
Jens
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