Thanks.
I now find that, when I copy (or cut) the re-con folder from SUBJECTS_DIR to the shared folder (with XP), it seems that no changes happen - the file format remains the same.
But if I restart the Xubuntu, and copy (or cut) this re-con folder from shared folder back to SUBJECTS_DIR, then the file format automatically changes and the re-con results can not be recognized. This is quite odd...
I have to move the re-con results to the shared folder because in the Xubuntu FSV5.1.0 virtual hard disk the space is only 10G. So to me now, if I can expand the disk to, say for example, 50G, then at least I don't need to move the re-con results but just save them in SUBJECTS_DIR, and so the file formats will not change.
On 7 June 2013 20:38, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
I meant for you to cat them and put them in the text of the email. Something is badly wrong with them. They should be simple text files with a 4x3 matrix and a couple of header lines. Not sure what happened but you will need to delete them and regenerat them
cheers Bruce
On Fri, 7 Jun 2013, huang bs wrote:
Seems that I can not post the attachements...
---------- Forwarded message ---------- From: huang bs huangbs@gmail.com Date: 5 June 2013 22:51 Subject: Re: [Freesurfer] problem about file format To: Bruce Fischl fischl@nmr.mgh.harvard.edu Cc: freesurfer@nmr.mgh.harvard.edu
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/**compliancelinehttp://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
freesurfer@nmr.mgh.harvard.edu
-
huang bs