Hi Paul
thanks for the clarification, the 178 time points would have been
shocking (but pretty cool!). I'll leave this for Martin to answer,
although you might try reposting in a week or two if he doesn't since
he's trying to finish something and pretty busy.
Bruce
On Sat, 19 Jan 2013, paul
horton wrote:
Sorry, that should be 4 separate anatomical scans of the same person
On 19 Jan 2013, at 03:57, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote:
Really? 178 separate anatomical scans of the same person?
On Jan 18, 2013, at 4:31 PM, paul horton <horton_p...@hotmail.com>
wrote:
Hi Bruce and Martin,
Thanks for your replies.
With regards to the questions from Bruce,
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
mris_volmask --label_left_white 2 --label_left_ribbon 3
--label_right_white 41 --label_right_ribbon 42
--save_ribbon --save_distance
PREDEP46C_fsf.long.PREDEP46_template
SUBJECTS_DIR is
/home/k0933235/paul/PREDEP_Structural/subjects2
loading input data...
hemi masks overlap voxels = 533537
writing
volume/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/mri/ribbon.mgz
writing ribbon files
#-----------------------------------------
#@# AParc-to-ASeg Tue Jan 15 05:45:35 GMT 2013
/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template
mri_aparc2aseg --s PREDEP46C_fsf.long.PREDEP46_template
--volmask
reading colortable from annotation file...
colortable with 36 entries read
(originally/autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fi
nal.txt)
reading colortable from annotation file...
colortable with 36 entries read
(originally/autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_fi
nal.txt)
SUBJECTS_DIR
/home/k0933235/paul/PREDEP_Structural/subjects2
subject PREDEP46C_fsf.long.PREDEP46_template
outvol/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/mri/aparc+aseg.mgz
useribbon 0
baseoffset 0
RipUnknown 0
Reading lh white surface
/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/surf/lh.white
Reading lh pial surface
/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/surf/lh.pial
Loading lh annotations
from/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/label/lh.aparc.annot
Reading rh white surface
/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/surf/rh.white
Reading rh pial surface
/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/surf/rh.pial
Loading rh annotations
from/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/label/rh.aparc.annot
Have color table for lh white annotation
Have color table for rh white annotation
Loading ribbon segmentation
from/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/mri/ribbon.mgz
Building hash of lh white
Building hash of lh pial
Building hash of rh white
Building hash of rh pial
Loading aseg
from/home/k0933235/paul/PREDEP_Structural/subjects2/PREDEP46C_fsf.long.PREDEP46
_template/mri/aseg.mgz
ASeg Vox2RAS: -----------
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
-------------------------
Labeling Slice
0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19
20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38
39
40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58
59
################################################
Thanks
Paul
____________________________________________________________________________
Date: Fri, 18 Jan 2013 14:59:06 -0500
From: mreu...@nmr.mgh.harvard.edu
To: horton_p...@hotmail.com
CC: al.hang...@yahoo.ca; Freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] FW: longitudinal analysis
Hi Paul,
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.
Best wishes
Paul
On 18 Jan 2013, at 16:40, "Alex Hanganu"
<al.hang...@yahoo.ca> wrote:
Hi Paul,
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: fis...@nmr.mgh.harvard.edu
> To: horton_p...@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:
fis...@nmr.mgh.harvard.edu
> > To: horton_p...@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.
> >
> >
_______________________________________________
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-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.
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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.
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Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________ 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.
_______________________________________________
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
_______________________________________________
Freesurfer mailing list
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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.
_______________________________________________
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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
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