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
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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: 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
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list
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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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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.hanganu@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: 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
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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.hanganu@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: 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. > > > >
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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.
_______________________________________________ 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.
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.hanganu@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: 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. > > > >
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Hi Bruce and Martin, Thanks for your replies. With regards to the questions from Bruce, 1.The machine has 72gb of ram2.There are no other processes running3.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_final.txt) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.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 PaulDate: Fri, 18 Jan 2013 14:59:06 -0500 From: mreuter@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: al.hanganu@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.hanganu@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: 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.
> >
> >
_______________________________________________
Freesurfer mailing list
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https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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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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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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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.
I dont know if this applies but I sometimes have really long run times when image quality is bad, usually from subject movement. I drop them. Josh
On Fri, Jan 18, 2013 at 1:31 PM, paul horton horton_paul@hotmail.comwrote:
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,
- 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_final.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.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: mreuter@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: al.hanganu@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.hanganu@yahoo.caal.hanganu@yahoo.cawrote:
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: 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. > > > >
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.
_______________________________________________ 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 listFreesurfer@nmr.mgh.harvard.eduhttps://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
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.
Really? 178 separate anatomical scans of the same person?
On Jan 18, 2013, at 4:31 PM, paul horton horton_paul@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,
- This is happening in the -long runs, but, only in 1 of the four runs of that subject.
- 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_final.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.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: mreuter@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: al.hanganu@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.hanganu@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: 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. > > > >
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.
_______________________________________________ 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 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
Sorry, that should be 4 separate anatomical scans of the same person
On 19 Jan 2013, at 03:57, "Bruce Fischl" fischl@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_paul@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,
- This is happening in the -long runs, but, only in 1 of the four runs of that subject.
- 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_final.txt)
reading colortable from annotation file...
colortable with 36 entries read (originally /autofs/space/amaebi_026/users/buckner_cortical_atlas/scripts/colortable_final.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: mreuter@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: al.hanganu@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.hanganu@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: 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. > > > >
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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" fischl@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_paul@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: mreuter@nmr.mgh.harvard.edu To: horton_paul@hotmail.com CC: al.hanganu@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.hanganu@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: 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. > > > > _______________________________________________ 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. _______________________________________________ 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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