New subject: WM/GM boundary changes and control points

14 Oct 2012


      I've been struggling to upload the file to the ftp server, but failed in
several times.
Sorry for bothering you, but I will send an e-mail when the uploading is
done.
Best,
EK
2012/10/14 Bruce Fischl fischl@nmr.mgh.harvard.edu
...
I found EK_test.zip, but neither tar nor unzip knows how to uncomress it.
What format is it? Or maybe it's corrupted...
On Sat, 13 Oct 2012, EK Kim wrote:
Bruce, and other experts, thank you for your time :)
...
I'm now uploading the data folder (before cp and after cp) to the
freesurfer incoming directory.
We obtained the 3D-SPGR axial images using 3T GE system which have
8HRBRAIN receiving coil.
Data acquisition matrix is 320-by192, FOV is 200-by-200.
Other parameters;
slice thickness =1.5
TR=5.924
TE=1.472
Flip angle: 20
Inversion Time=400
Imaging Frequency 127.88
Percent Phase FOV =80
Sincerely,
EK
2012/10/11 Bruce Fischl fischl@nmr.mgh.harvard.edu
      Hi EK
  that is a really low-contrast image. Can you tell me about the

acquisition parameters and resolution? Also, I can't
      diagnose your problem from just the volume I'll need the entire
(tarred and gzipped) subject directory. Finally,
      please cc the list on these emails so that others can help you!
  Bruce
  On Thu, 11 Oct 2012, EK Kim wrote:

        I uploaded the files to transfer/incoming folder.


        Best,

        EK

        2012/10/11 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
              If you upload the subject to our FTP site I will take a

look
            Bruce
        On Oct 10, 2012, at 9:29 PM, EK Kim <ksea03@gmail.com> wrote:

              Thank you for your answer.
        I'm not sure I understand your question right,
        but I just processed the file using following procedures.
        1. recon-all -autorecon1 -nuintensitycor-3T (because mine was
        3T)
        2. skullstripping brain mask using gcuts
        3. adding control points (only on the left hemisphere)
        4. recon-all -autorecon2-cp
        and this figure was made by a commnad line, [tkmedit wm.mgz

-aux
            brain.mgz -surfs].
            Best,
            EK.
        2012/10/10 Bruce Fischl <fischl@nmr.mgh.harvard.edu>
              what was the name of the file that you transferred?
              On Wed, 10 Oct 2012, EK Kim wrote:

                    I already uploaded this problem 2 days
                    ago, reprocessing the subject to make
                    sure about control points.
                    However when I added the control points
                    to the left hemisphere,
                    the right hemisphere surface was changed
                    severely.
                    I used the command line, recon-all
                    -autorecon2-cp -s subjectID.
                    Could you tell me why does it occur and
                    how to deal with it?


                    Best,

                    EK


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Re: [Freesurfer] WM/GM boundary changes and control points