Re: [Freesurfer] recon-all completes without all the info..
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
Re: [Freesurfer] recon-all completes without all the info..
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
Re: [Freesurfer] recon-all completes without all the info..
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.edumailto: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.
Re: [Freesurfer] recon-all completes without all the info..
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 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.
Re: [Freesurfer] recon-all completes without all the info..
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
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
