Hello all,
I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
Any suggestions as to why this is happening?
Nathan
What version of freesurfer are you using now and what version was used to process the data? I suspect mixed versions were used. You can rerun with the -clean-aseg flag to start again.
On Wed, 2009-02-11 at 10:43 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
Any suggestions as to why this is happening?
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Yes, the versions are different. I am not sure of the exact version numbers, but I believe they are the 2 most recent releases. Do I need to run the scans from autorecon1 with the clean-aseg command, or can I run them from later processing steps? Thanks for your help,
Nathan
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 2/11/2009 11:53 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] exited with errors
What version of freesurfer are you using now and what version was used to process the data? I suspect mixed versions were used. You can rerun with the -clean-aseg flag to start again.
On Wed, 2009-02-11 at 10:43 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
Any suggestions as to why this is happening?
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
they can be started from the -autorecon2 stage (also include - autorecon3).
On Wed, 2009-02-11 at 12:05 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Yes, the versions are different. I am not sure of the exact version numbers, but I believe they are the 2 most recent releases. Do I need to run the scans from autorecon1 with the clean-aseg command, or can I run them from later processing steps? Thanks for your help,
Nathan
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 2/11/2009 11:53 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] exited with errors
What version of freesurfer are you using now and what version was used to process the data? I suspect mixed versions were used. You can rerun with the -clean-aseg flag to start again.
On Wed, 2009-02-11 at 10:43 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
Any suggestions as to why this is happening?
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
I attempted to re-run using the -clean-aseg flag, but this time got an error which said:
ERROR: cannot find [subject path]/mri/aseg.mgz
Is the underlying problem that I used two different versions? Should I sync up the two versions (one is on a server and one is on my desktop) in order to avoid this issue altogether?
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 2/11/2009 12:43 PM To: Dankner, Nathan (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: RE: [Freesurfer] exited with errors
they can be started from the -autorecon2 stage (also include - autorecon3).
On Wed, 2009-02-11 at 12:05 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Yes, the versions are different. I am not sure of the exact version numbers, but I believe they are the 2 most recent releases. Do I need to run the scans from autorecon1 with the clean-aseg command, or can I run them from later processing steps? Thanks for your help,
Nathan
-----Original Message----- From: Nick Schmansky [mailto:nicks@nmr.mgh.harvard.edu] Sent: Wed 2/11/2009 11:53 AM To: Dankner, Nathan (NIH/NIMH) [F] Cc: Freesurfer Mailing List Subject: Re: [Freesurfer] exited with errors
What version of freesurfer are you using now and what version was used to process the data? I suspect mixed versions were used. You can rerun with the -clean-aseg flag to start again.
On Wed, 2009-02-11 at 10:43 -0500, Dankner, Nathan (NIH/NIMH) [F] wrote:
Hello all,
I have recently been running some scans with very few defects, but have been encountering a particular error message on occasion when I try to run it through autorecon2 and autorecon3 after a bit of manual correction. The error output is:
MRI_fill: could not read segmentation from aseg.auto_noCC.mgz reading segmented volume aseg.auto_noCCseg.mgz... ERROR: cannot find [subject path]/aseg.auto_noCCseg.mgz No such file or directory
Any suggestions as to why this is happening?
Nathan
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Dankner, Nathan (NIH/NIMH) [F] -
Nick Schmansky