Hi Pradeep sorry, I meant autorecon1 and autorecon2 (but not autorecon3)
cheers Bruce On Tue, 9 Dec 2014, pradeep mahato wrote: > Hi Bruce, > > I am using Intel Core 2 Quad core processor 2.2 GHz with 4 GB ram. > The version i am using is freesurfer-i686-redhat-linux-gnu-stable5-20130513 > Using autorecon2 process , I got error saying nu.mgz file is missing. Error > : mghRead(/home/nsb/oasis/OAS2_RAW_PART1/OAS1_2/mri/nu.mgz, -1): could not > open file > Should I include nuintensitycor. > > Thanks > > Pradeep > > On Mon, Dec 8, 2014 at 7:01 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> > wrote: > Hi Pradeep > > you could only run recon-all -autorecon2 instead of -all which > should > save you some time. 30 hours is pretty long though. What > hardware are you > using? If you have a modern Linux box with say 4-8 cores it > should take > less than 10. Or with 2 cores and >4G of ram you could run 2 > recons at the > same time. What version of FS are you using? The newer ones use > openmp, > although only the dev version has a bunch of things that take > advantage of > it. If you want to use more than one core try using -openmmp 4 > (to use 4 > cores). > > cheers > Bruce > > > On Mon, 8 Dec 2014, pradeep mahato wrote: > > > Hello, > > > > I need to extract Hippocampus from brain mri image. The > recon-all process > > takes more than 30 hours to reconstruct from an single image. > I am having an > > dataset of 200 subjects, it is not feasible to run the recon > process for all > > individual brain mri images. > > Is there any method to possibly get the hippocampus segmented > and get the > > statistical values faster and efficient way. > > > > Thanking You > > > > Pradeep Kumar Mahato > > > > > _______________________________________________ > 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. > > > > > -- > Pradeep Kumar Mahato > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
