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_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: 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. >> >> >> _______________________________________________ >> 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 > _______________________________________________ > 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.
_______________________________________________ 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.
