Thank you Bruce, I certainly understand your point. In my study I am trying to use whole brain volume to normalize my volumetrics data. Due to the inclusion of the dura into brain, I may get variation in the whole brain volume across subjects. In addition the current issue is affecting the graymatter/whitematter boundary that will also bring variation in the cortical thickness measurements. That is the reason I was trying to get good skull stripping.
Your suggestions and guidance will help me. Thanks, Rashmi. On 10/2/12 2:05 PM, "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> wrote: >Hi Rashmi > >getting rid of all the dura without removing any problem is exceedingly >difficult (if not impossible). Usually we live with some remaining dura >as it doesn't affect the surface placement much. > >cheers >Bruce >On Tue, 2 Oct 2012, Rashmi >Singh wrote: > >> Hello experts, >> I am getting skull strip issues with FreeSurfer recon-all runs in every >> data. >> I ran recon-all on my T1-data and noticed that the skullstrip is not so >> good. Almost in every subjects there were dura included, so I tried the >> suggestion of using the flags -skullstrip and -Clean?bm and ?gcut in my >> recon-all command line for one subject. Forexmaple: >> I ran reconall using the following command lin: >> recon-all ?skullstrip first -clean?bm ?gcut ?sAA***.T* -all >>-use?mritotal >> >> The run was complete and I looked at the brainmask.mgz file of the >>output. >> But I didn't see any correction. >> I am attaching the jpg image of the sagittal view of brainmask.nii ( I >> converted the mgz file to nii to view tham in afni) >> SubjFS: is the image from recon-all run >> SubjFS: is the image from recon-all that was run with >> Skullstrip/clean-bm/gcut options included. >> >> Did I do anything wrong? >> Your guidance and suggestion needed. >> Thanks, >> Rashmi. >> >> > > >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 . 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
