Hi Sudhin, You will need to add -autorecon2 and -autorecon3 to the command you ran before, or just replace all -autorecon# flags with the -all flag.
for new subjects: recon-all -s xyx -i xyz -autorecon1 -autorecon2 -autorecon3 for subjects who already have completed autorecon1: recon-all -s xyx -autorecon2 -autorecon3 The T1 and brainmask volumes should already exist after completing autorecon1. The rest of those files are creating during autorecon2 and autorecon3. -Louis On Thu, 9 May 2013, Sudhin A. Shah wrote: > Hi! I am running this on ~26 datasets and some have exited with errors and > others have not completed (~ 2 days). > > Sorry, but what should I be running to get the following files? > > 1) T1.mgz > 2) wm.mgz > 3) aparc+aseg.mgz > 4) brainmask.mgz > 5) ribbon.mgz > 6) And I need to run reg-feat2anat > > I am quite certain that what I ran (successfully) before > > was recon-all -s xyx -i xyz -autorecon1 but when I ran this recently, all the > files above did not populate. > > > ________________________________________ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke > [vi...@nmr.mgh.harvard.edu] > Sent: Tuesday, May 07, 2013 12:05 PM > To: Sudhin A. Shah > Cc: Freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] recon-all completes without all the info.. > > Yes, the -all flag will run autorecon1, autorecon2, and autorecon3. > > recon-all -all -i <path to dicom/nii/mgz T1 image> -s <subjID> > > For that uncompleted subject you have though if sounds like you just need > to run autorecon2 and 3 > > recon-all -autorecon2 -autorecon3 -s <subjID> > > On Tue, 7 May 2013, Sudhin A. Shah wrote: > >> Is there 1 command line? I used to just run the 1 line. >> >> >> >> On May 7, 2013, at 10:19 AM, "Louis Nicholas Vinke" >> <vi...@nmr.mgh.harvard.edu> wrote: >> >>> Hi Sudhin, >>> You'll need to also run -autorecon2 and -autorecon3 in order to get >>> surfaces and all the cortical/sub-cortical measures. >>> -Louis >>> >>> On Tue, 7 May 2013, Sudhin A. Shah wrote: >>> >>>> On May 6, 2013, at 3:05 PM, Sudhin A. Shah wrote: >>>> >>>> Hi, This is a new issue as it used to run well before.. I run >>>> recon-all ... ... -autorecon1 - force and it completes without >>>> error but I don't have all the files.. >>>> >>>> Attached is a screenshot. On the right is the output from a file >>>> that worked before and on the left is a newer folder.. >>>> <Screenshot.png>_______________________________________________ >>>> 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
