Dear freesurfer users,
I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called PTpost_P04.
First I tried: recon-all autorecon1 s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
I became the error message: could not read 65536 bytes at slice 76
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
It would be great if anybody could help me in solving this.
Best regards Sandra
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Hi Sandra
can you check to make sure that you have enough disk space and that that partition isn't full?
cheers Bruce On Wed, 9 Jan 2013, Sandra Preissler wrote:
Dear freesurfer users,
I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called ?PTpost_P04?.
First I tried: recon-all ?autorecon1 ?s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
I became the error message: ?could not read 65536 bytes at slice 76?
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
It would be great if anybody could help me in solving this.
Best regards Sandra
This message was sent through https://webmail.uni-jena.de
Hi Bruce,
Thanks for your fast reply. I checked it again and there is 131 GB disk space free on the device.
Best regards Sandra
Zitat von Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Sandra
can you check to make sure that you have enough disk space and that that partition isn't full?
cheers Bruce On Wed, 9 Jan 2013, Sandra Preissler wrote:
Dear freesurfer users,
I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called ?PTpost_P04?.
First I tried: recon-all ?autorecon1 ?s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
I became the error message: ?could not read 65536 bytes at slice 76?
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
It would be great if anybody could help me in solving this.
Best regards Sandra
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Hi Sandra, Have you taken a look at the T1.mgz volume to see if there is anything peculiar? -Louis
On Wed, 9 Jan 2013, Sandra Preissler wrote:
Hi Bruce,
Thanks for your fast reply. I checked it again and there is 131 GB disk space free on the device.
Best regards Sandra
Zitat von Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Sandra
can you check to make sure that you have enough disk space and that that partition isn't full?
cheers Bruce On Wed, 9 Jan 2013, Sandra Preissler wrote:
Dear freesurfer users,
I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called ?PTpost_P04?.
First I tried: recon-all ?autorecon1 ?s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
I became the error message: ?could not read 65536 bytes at slice 76?
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
It would be great if anybody could help me in solving this.
Best regards Sandra
This message was sent through https://webmail.uni-jena.de
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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or try deleting the T1.mgz and running recon-all -make all
cheers Bruce
On Sat, 12 Jan 2013, Louis Nicholas Vinke wrote:
Hi Sandra, Have you taken a look at the T1.mgz volume to see if there is anything peculiar? -Louis
On Wed, 9 Jan 2013, Sandra Preissler wrote:
Hi Bruce,
Thanks for your fast reply. I checked it again and there is 131 GB disk space free on the device.
Best regards Sandra
Zitat von Bruce Fischl fischl@nmr.mgh.harvard.edu:
Hi Sandra
can you check to make sure that you have enough disk space and that that partition isn't full?
cheers Bruce On Wed, 9 Jan 2013, Sandra Preissler wrote:
Dear freesurfer users,
I have an unexpected error using autorecon1. The error occurred during the skull stripping process of a person called ?PTpost_P04?.
First I tried: recon-all ?autorecon1 ?s PTpost_P04 After the first error (recon-all -s PTpost_P04 exited with ERRORS) I checked the logfile and tried the following: cd /mnt/bp13dat/Studie43_Phantom_Arm/Statistik/4_MRT/freesurfer/PTpost_P04/mri
followed directly by: mri_watershed -keep brainmask.auto.mgz brainmask.mgz brainmask.mgz -T1 -brain_atlas /opt/freesurfer/average/RB_all_withskull_2008-03-26.gca transforms/talairach_with_skull.lta T1.mgz brainmask.auto.mgz
I became the error message: ?could not read 65536 bytes at slice 76?
The information about the freesurfer version and linux version used are: FREESURFER_HOME: /opt/freesurfer Build stamp: freesurfer-Linux-centos4_x86_64-stable-pub-v5.1.0 Kernel info: Linux 2.6.34.10-0.6-default x86_64
It would be great if anybody could help me in solving this.
Best regards Sandra
This message was sent through https://webmail.uni-jena.de
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.
This message was sent through https://webmail.uni-jena.de
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Sandra Preissler