Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: *tkregister2 --mgz --s linziyi --fstal --surf orig* The terminal then reports: *ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File* This file *talairach.xfm* does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
Dear Bruce,
Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi.
One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/subjects ? If possible, I don't want to move the data to the shared folder and then face such problem.
Sorry I am quite new to Linux so some questions may be quite stupid.
Thank you very much!
On 05/06/2013, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
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 file is definitely wrong. Something is happening when you move the files back and forth. This is beyond our scope to help you with, unless someone knows of the top of their head what is going on. Check with your system administrator. doug
On 06/05/2013 10:51 AM, huang bs wrote:
Dear Bruce,
Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi.
One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/subjects ? If possible, I don't want to move the data to the shared folder and then face such problem.
Sorry I am quite new to Linux so some questions may be quite stupid.
Thank you very much!
On 05/06/2013, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
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
Let me send you again the files because in the previous reply the attachments were more than 500k.
On 05/06/2013, huang bs huangbs@gmail.com wrote:
Dear Bruce,
Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi.
One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/subjects ? If possible, I don't want to move the data to the shared folder and then face such problem.
Sorry I am quite new to Linux so some questions may be quite stupid.
Thank you very much!
On 05/06/2013, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
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.
-- Best Regards,
Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong
On 05/06/2013, huang bs huangbs@gmail.com wrote:
Let me send you again the files because in the previous reply the attachments were more than 500k.
On 05/06/2013, huang bs huangbs@gmail.com wrote:
Dear Bruce,
Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi.
One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/subjects ? If possible, I don't want to move the data to the shared folder and then face such problem.
Sorry I am quite new to Linux so some questions may be quite stupid.
Thank you very much!
On 05/06/2013, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
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.
-- Best Regards,
Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong
-- Best Regards,
Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong
There is still something wrong with these files. Probably a problem with copying it back and forth. doug
On 06/05/2013 08:19 PM, huang bs wrote:
Let me send you again the files because in the previous reply the attachments were more than 500k.
On 05/06/2013, huang bs huangbs@gmail.com wrote:
Dear Bruce,
Yes, sure. I printed the screens and showed you two cases. One can be recognized, the other one can not. Please find attached for the six figures. I also attached the files talairach.xfm and talairach.auto.xfm for the subject linziyi.
One more question: how to extend the hard disk space in Xubuntu, especially in the folder /home/virtualuser/freesurfer/subjects ? If possible, I don't want to move the data to the shared folder and then face such problem.
Sorry I am quite new to Linux so some questions may be quite stupid.
Thank you very much!
On 05/06/2013, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
no, I haven't seen that before. Can you cat /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm
and send us the contents?
Bruce On Wed, 5 Jun 2013, huang bs wrote:
Hi All,
Sorry to take up your time.
My freesurfer now can not recognize the re-con files (such as the .mgz files, or .xfm files, etc). For example, I run this command to check the talairach transform: tkregister2 --mgz --s linziyi --fstal --surf orig The terminal then reports: ERROR: /home/virtualuser/freesurfer/subjects/linziyi/mri/transforms/talairach.xfm does not start as 'MNI Transform File This file talairach.xfm does exist. But under Xubuntu, this talairach.auto.xfm file has a different icon and appears as "executable file". That's quite strange because I did not make such change to it.
These files did work when I just finished the re-con. But afer the re-con, I moved them from the freesurfer subjects folder to the shared folder (shard with XP), because the freesurfer subjects folder has a limited space. After a few days, I moved them back to the subjects folder for doing the statistical analysis, and then I have such problem. Even under the shared folder, the files can not be read either.
For the cases I just re-con, since they are not moved to elsewhere, everything seems OK.
Have you guys had such problem before and how to fix it? Thanks!
-- Best Regards,
B Huang
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.
-- Best Regards,
Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
Bruce Fischl -
Douglas N Greve -
huang bs