Hello
I also get similar problem : the diffusion data are quite to big. I had
to repeat the bedpostx 2 or 3 times in order to make it complete.
So I guess it depend of the load of each node. It was not killed by the
sge for any ressource limit, but it was kill by the processor because of
memory issue I guess (so I could not see it on the cluster log file)
I had a similar problem when trying to do probtrackx. (the jobs were
kill by the cluster) The solution was just to ask a big amount of memory
(qsub -l mem=12gb) so that the cluster will only run one or two
probtrack process on the same node.
I do not know how to change fslsub so that bedpostx add the extra
argument to qsub (ie : -l mem=...)
You can also use qalter as suggest by Colin, but then you have to be
quick to make the qalter during the preproc step, before each element of
the array start.
Cheers
Romain
Le 17/10/2013 00:24, Huang Su-Chun a écrit :
You are right, the missing slices mainly located in the middle of the
brain. So I guess the problem comes from our grid engine....
I tried use -nf=3, but the process fails all the time. I guess it too
demanding for the computer
Thank you,
Su
2013/10/16 Glasser, Matthew <[email protected]
<mailto:[email protected]>>
Do you know that your cluster is not killing some of the jobs?
Which slices are missing? If it is mainly the middle ones, I'd
suspect that they are exceeding some limit for the cluster.
For HCP data you can successfully model 3 fibers (--nf=3) and
should use the -g option with FSL 5.0.5. I'd leave fudge and bi
at their defaults unless you have a reason to change them.
--model=2 is correct.
Peace,
Matt.
From: Huang Su-Chun <[email protected]
<mailto:[email protected]>>
Date: Wednesday, October 16, 2013 4:27 PM
To: Matt Glasser <[email protected]
<mailto:[email protected]>>
Cc: Stamatios Sotiropoulos <[email protected]
<mailto:[email protected]>>, "[email protected]
<mailto:[email protected]>"
<[email protected]
<mailto:[email protected]>>
Subject: Re: [HCP-Users] BedpostX failed
It happened on subject 100307 and 105115. I am running the job in
a grid engine.
The command line I use is listed below:
bedpostx
/NAS_II/Public-Data/Parcellation/Q2_released_data/105115/105115_Diffusion_preproc/T1w/Diffusion
--nf=2 --fudge=1 --bi=1000 --model=2
Thank you,
Su
2013/10/15 Glasser, Matthew <[email protected]
<mailto:[email protected]>>
What subject is this?
What command line did you call bedpostx with?
Are you running this on your local machine or in some cluster
environment?
Note that a new version of FSL was just released with
improvements to bedpostx that you need to correctly process
HCP data (not fixing missing slices, but correcting for the
effects of gradient nonlinearities on the bmatrix), so I
highly recommend you update.
Peace,
Matt.
From: Huang Su-Chun <[email protected]
<mailto:[email protected]>>
Date: Tuesday, October 15, 2013 6:12 PM
To: Stamatios Sotiropoulos <[email protected]
<mailto:[email protected]>>
Cc: "[email protected]
<mailto:[email protected]>"
<[email protected]
<mailto:[email protected]>>
Subject: Re: [HCP-Users] BedpostX failed
Hi Stam,
I checked the bedpostX results and it didn't have the same
number of slices as the input data. It caused problem when I
want to to probabilistic tracking. And this missing slices
problem happens quite a lot!
Thank you,
Su
2013/10/15 Stamatios Sotiropoulos <[email protected]
<mailto:[email protected]>>
Hi
Is it just the message that worries you? Have you checked
whether bedpostx results have the same number of slices as
the input data? Notice that the diffusion data are
transferred to T1 space and lots of inferior/superior
slices may be empty.
Cheers
Stam
On 15 Oct 2013, at 04:47, Huang Su-Chun
<[email protected] <mailto:[email protected]>> wrote:
Hi dear experts,
I am running bedpostX on the HCP diffusion data, however,
it seems that sometimes (60% of chance) the bedpostX
ended before finishing all the slices. Take the HCP data
for example, it should have 145 slices, but the betpostX
stopped at slice 103 then show a message said "All slice
processed."
Does anyone know where the problem might be? Thank you!
Cheers,
Su
--
Su-Chun Huang
Research Scientist
Integrated Brain Imaging Center
Department of Radiology
University of Washington
Seattle, WA 98195
phone: 206-687-0113 <tel:206-687-0113>
_______________________________________________
HCP-Users mailing list
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<mailto:[email protected]>
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--
Su-Chun Huang
Research Scientist
Integrated Brain Imaging Center
Department of Radiology
University of Washington
Seattle, WA 98195
phone: 206-687-0113 <tel:206-687-0113>
_______________________________________________
HCP-Users mailing list
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<mailto:[email protected]>
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--
Su-Chun Huang
Research Scientist
Integrated Brain Imaging Center
Department of Radiology
University of Washington
Seattle, WA 98195
phone: 206-687-0113 <tel:206-687-0113>
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The materials in this message are private and may contain
Protected Healthcare Information or other information of a
sensitive nature. If you are not the intended recipient, be
advised that any unauthorized use, disclosure, copying or the
taking of any action in reliance on the contents of this
information is strictly prohibited. If you have received this
email in error, please immediately notify the sender via telephone
or return mail.
--
Su-Chun Huang
Research Scientist
Integrated Brain Imaging Center
Department of Radiology
University of Washington
Seattle, WA 98195
phone: 206-687-0113
_______________________________________________
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