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_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><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 > listfreesur...@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. > >
_______________________________________________ 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.
