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 <fis...@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 <fis...@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 <kse...@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 <fis...@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 >> >> >> >> >> 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. >> >> >> ______________________________**_________________ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> >> >>
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