1.The machine has 72gb of ram 2.There are no other processes running 3.There are 178 time points.
With regards to the questions from Martin,
1. This is happening in the -long runs, but, only in 1 of the four runs of that subject. 2. I have added a part of the log below. I am not sure if its 'mris_volmask' or 'mri_aparc2aseg' running.
################################# /home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46_template/mri
also, is this happening in the -base run or in one of the -long runs
(or in all of the -long runs of that subject). What binary is
running so slowly (you mentioned some output "labelling slice", can
you scroll up in the log and see what exactly is running)?
Best, Martin
On 01/18/2013 02:46 PM, Bruce Fischl
wrote:
how much RAM do you have in the machine? And are there
other processes running at the same time? How many timepoints does
the subject have?
Bruce
On Fri, 18 Jan 2013, paul horton wrote:
Hi Alex,
Thanks for your reply.
I am also using Linux. I have restarted the analysis a few times
but the
process for this particular subject is very slow. When I try the
same
analysis on a different subject using the same machine, it only
takes a few
hours. So not sure why the analysis is having problems with
this particular
subject.
I also had such problems previously. My initial analyses
were
performed on mac. Though it might seem strange, some
analyses
resolved after I just restarted the computer. Other ones I
analysed on centos. Now I am doing all the recons on
linux.
best wishes,
Alex.
Le 1/18 9:22, paul horton a écrit :
> Date: Fri, 18 Jan 2013 08:54:48 -0500
> From: fischl@nmr.mgh.harvard.edu
> To: horton_paul@hotmail.com
> Subject: RE: [Freesurfer] longitudinal analysis
>
> Hi Paul
>
> can you cc the list so that others can answer?
>
> thanks
> Bruce
> On Fri, 18 Jan 2013, paul
> horton wrote:
>
> > Hi Brian,
> >
> > Thanks for your reply.
> >
> > I am running freesurfer 4.5.0. We are using the
older
version so that the
> > analyses performed are the same across subjects.
> >
> > Best wishes
> >
> > Paul
> >
> > Date: Fri, 18 Jan 2013 08:21:05 -0500
> > From: fischl@nmr.mgh.harvard.edu
> > To: horton_paul@hotmail.com
> > CC: freesurfer@nmr.mgh.harvard.edu
> > Subject: Re: [Freesurfer] longitudinal analysis
> >
> > Hi Paul
> >
> > what is the actual binary being run?
> >
> > Bruce
> > On Fri, 18 Jan 2013, paul horton wrote:
> >
> > > Hi guys,
> > >
> > > I am currently running a longitudinal
analysis on a
set of scan. It is
> > > currently running and so far it has taken 5
days. It
seems to be taking a
> > > large amount of time on a process called
labelling
slice. I have run the
> > > same analysis on other subjects which took
about 6
hours to complete. So
> > I
> > > was wondering if you know of any reason
why a set of
scans would take long
> > er
> > > to process than others. I have checked the
inital
scans and nothing seems
> > > obviously wrong with them.
> > >
> > > Best Wishes
> > >
> > > Paul
> > >
> > >
> >
> > _______________________________________________
Freesurfer mailing list
> > Freesurfer@nmr.mgh.harvard.edu
> >
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information
> > in this e-mail is intended only for the person
to whom
it is addressed. If
> > you believe this e-mail was sent to you in error
and
the e-mail contains
> > patient information, please contact the Partners
Compliance HelpLine at
> > http://www.partners.org/complianceline . If the
e-mail
was sent to you in
> > error but does not contain patient information,
please
contact the sender
> > and properly dispose of the e-mail.
> >
> >
The information in this e-mail is intended only for the person
to whom it is
addressed. If you believe this e-mail was sent to you in error
and the e-mai
l
contains patient information, please contact the Partners
Compliance HelpLin
e at
http://www.partners.org/complianceline . If the e-mail was sent
to you in er
ror
but does not contain patient information, please contact the
sender and prop
erly
dispose of the e-mail.
The information in this e-mail is intended only for the
person
to whom it is
addressed. If you believe this e-mail was sent to you in
error
and the e-mail
contains patient information, please contact the Partners
Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was
sent
to you in error
but does not contain patient information, please contact
the
sender and properly
dispose of the e-mail.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.