Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
You did not run it all the way through (you stopped at autorecon2) doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu mailto:greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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.
Hi Doug, I tried running autorecon2 after successful autorecon1, however it crashed. I could not figure out why it crashed and how to fix it. Any suggestions. I've attached log file of autorecon2
-Sabin
On Tuesday, February 25, 2014 10:47 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You did not run it all the way through (you stopped at autorecon2) doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects
finished without any error.
However in few subjects directory, labels
sub-directory only have
lh.cortex.label and rh.cortex.label and not other
label files like
*.label and *.annot. Could anyone help me on how
to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Hi Sabin, What command did you run? Sending the recon-all.log file in the scripts dir might be a little more helpful. It's failing because the ribbon.mgz does not exist which requires surfaces.
This thread might be relevant: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876.html
-Louis
On Wed, 26 Feb 2014, sabin khadka wrote:
Hi Doug, I tried running autorecon2 after successful autorecon1, however it crashed. I could not figure out why it crashed and how to fix it. Any suggestions. I've attached log file of autorecon2
-Sabin
On Tuesday, February 25, 2014 10:47 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You did not run it all the way through (you stopped at autorecon2) doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
yep, you'll need a new version of mri_segstats, which you can find by following the thread that Louis posted doug On 02/26/2014 12:32 PM, Louis Nicholas Vinke wrote:
Hi Sabin, What command did you run? Sending the recon-all.log file in the scripts dir might be a little more helpful. It's failing because the ribbon.mgz does not exist which requires surfaces.
This thread might be relevant: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876.html
-Louis
On Wed, 26 Feb 2014, sabin khadka wrote:
Hi Doug, I tried running autorecon2 after successful autorecon1, however it crashed. I could not figure out why it crashed and how to fix it. Any suggestions. I've attached log file of autorecon2
-Sabin
On Tuesday, February 25, 2014 10:47 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You did not run it all the way through (you stopped at autorecon2) doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
Hi Nicholas, Please see attached for recon-all.log. Thanks for your help. -Sabin
On Wednesday, February 26, 2014 12:36 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
yep, you'll need a new version of mri_segstats, which you can find by following the thread that Louis posted doug On 02/26/2014 12:32 PM, Louis Nicholas Vinke wrote:
Hi Sabin, What command did you run? Sending the recon-all.log file in the scripts dir might be a little more helpful. It's failing because the ribbon.mgz does not exist which requires surfaces.
This thread might be relevant: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg32876.html
-Louis
On Wed, 26 Feb 2014, sabin khadka wrote:
Hi Doug, I tried running autorecon2 after successful autorecon1, however it crashed. I could not figure out why it crashed and how to fix it. Any suggestions. I've attached log file of autorecon2
-Sabin
On Tuesday, February 25, 2014 10:47 AM, Douglas Greve greve@nmr.mgh.harvard.edu wrote:
You did not run it all the way through (you stopped at autorecon2) doug
On 2/25/14 9:00 AM, sabin khadka wrote:
Thanks Doug. recon-all.log is attached herewith.
On Monday, February 24, 2014 5:07 PM, Douglas N Greve greve@nmr.mgh.harvard.edu wrote:
are you sure it did not fail? Can you post the recon-all.log file to the list?
On 02/24/2014 04:22 PM, sabin khadka wrote:
Hi all, I ran recon-all -all and all the subjects finished without any error. However in few subjects directory, labels sub-directory only have lh.cortex.label and rh.cortex.label and not other label files like *.label and *.annot. Could anyone help me on how to fix this.
-Sabin
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Douglas N. Greve, Ph.D. MGH-NMR Center greve@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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.
freesurfer@nmr.mgh.harvard.edu
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Douglas Greve -
Douglas N Greve
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Louis Nicholas Vinke -
sabin khadka