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 <fis...@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 <huan...@gmail.com> >> Date: 5 June 2013 22:51 >> Subject: Re: [Freesurfer] problem about file format >> To: Bruce Fischl <fis...@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 <fis...@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<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 >> >> -- Best Regards, Bingsheng Huang Postdoctoral Research Fellow Diagnostic Radiology, The University of Hong Kong
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