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-bounces@nmr.mgh.harvard.edu [freesurfer-bounces@nmr.mgh.harvard.edu] on behalf of Louis Nicholas Vinke [vinke@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" vinke@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.
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