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
>>
>>
>>
>
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--
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