External Email - Use Caution
Hello,
Our lab has been using Freesurfer 5.3 for it's ongoing longitudinal study. I attempted to quality check one of our brains using tkmedit - I usually don't have any issues following our pipeline or running the tool. This time I received this message:
ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... :
I'm not sure where the xdebug file is located - it isn't anywhere in our Freesurfer directory in the server. Where can I find this file, and how can I fix this error? I've tried trouble shooting with some solutions I've seen in the archive. We have checked permissions, I use a PC - not a mac, and I have checked the main freesurfer directories as well as the directories associated with the brain I want to check. I have also tried to open other brains in the viewer resulting in the same error message. Is there a fix for this - ideally, one that doesn't require switching Freesurfer versions?
Thanks for any help you can provide!
Vincent Edwards
External Email - Use Caution
we are not supporting tkmedit anymore (and have not for a long time). Have you tried using freeview (or tkmeditfv which is a frontend for freeview that takes tkmedit-like options). FV is not available in 5.3, but you can still use it on 5.3 data.
On 8/4/2023 3:35 PM, Edwards, Vincent wrote:
External Email - Use Caution
Hello,
Our lab has been using Freesurfer 5.3 for it's ongoing longitudinal study. I attempted to quality check one of our brains using tkmedit - I usually don't have any issues following our pipeline or running the tool. This time I received this message:
ERROR: A segfault has occurred. This is not your fault, : but is most likely an unrecoverable error and has : made the program unstable. : : Please send the contents of the file .xdebug_tkmedit : that should be in this directory to freesurfer@nmr.mgh.harvard.edu : : Now exiting... :
I'm not sure where the xdebug file is located - it isn't anywhere in our Freesurfer directory in the server. Where can I find this file, and how can I fix this error? I've tried trouble shooting with some solutions I've seen in the archive. We have checked permissions, I use a PC - not a mac, and I have checked the main freesurfer directories as well as the directories associated with the brain I want to check. I have also tried to open other brains in the viewer resulting in the same error message. Is there a fix for this - ideally, one that doesn't require switching Freesurfer versions?
Thanks for any help you can provide!
Vincent Edwards
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-bz0wpn-WRKyx9EemFwuxOauwyW_6tVt7cjrGNX8qoA9Vk...
freesurfer@nmr.mgh.harvard.edu
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Douglas N. Greve -
Edwards, Vincent