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
