hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon
Hi Jon
what were the errors? We will want to fix them prior to official release.
thanks Bruce On Mon, 28 Jan 2013, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Jon,
If the error is where the perirhinal labels cannot be found in the fsaverage that sits in your subjects dir, then that issue was fixed on a more recent beta 5.2. recon-all now checks if the perirhinal labels exist in the fsaverage found in the subjects dir (which might not be the case if running on prior data where the copy of fsaverage was made) and if the labels do not exist it creates a new link. What that this issue? or a new one?
Nick
On Mon, 2013-01-28 at 14:50 -0500, Bruce Fischl wrote:
Hi Jon
what were the errors? We will want to fix them prior to official release.
thanks Bruce On Mon, 28 Jan 2013, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon _______________________________________________ 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
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed.
jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon _______________________________________________ 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.
Also, could I have a link for the centos4 of this updated version of 5.2? And is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically?
jon On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote:
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed.
jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon _______________________________________________ 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
updated 5.2 versions for centos4_x86_64 and macos lion are here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.2.0-BETA/
an updated centos4 build (32b) will not be ready until tomorrow.
n.
On Mon, 2013-01-28 at 15:29 -0500, Jonathan Holt wrote:
Also, could I have a link for the centos4 of this updated version of 5.2? And is there a working 5.2 for Mac OS X, 10.7 or 10.8 specifically?
jon On Jan 28, 2013, at 3:19 PM, Jonathan Holt wrote:
Nick,
it was in fact an error with missing perirhinal cortex labels in fsaverage. It did not exist, and then the process exited. Good to know it's been fixed.
jon On Jan 28, 2013, at 2:48 PM, Jonathan Holt wrote:
hello all,
Just for reference, we were having an issue with recon-all v 5.2 exiting with errors due to issues with the perirhinal cortex. We were able to simply commented out the parts of the script dealing with the perirhinal cortex. Just an FYI to those who may be having a similar problem.
Jon _______________________________________________ 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@nmr.mgh.harvard.edu
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Bruce Fischl -
Jonathan Holt -
Nick Schmansky