Hi Rashmi, I assume you've read the skullstrip wiki page, but I've included it below just in case.
Have you tried different watershed thresholds? Also, you do not need to include the -clean-bm flag every time. You can run the skullstrip step once with the -clean-bm to start from scratch, and the run skullstripping again without the -clean-bm flag so that you are performing additional skullstripping on the output from the last run. So something like this: first: recon-all -skullstrip -clean-bm -s <subj_ID> second run: recon-all -skullstrip -s <subj_ID> or maybe some variant of those commands where you are also specifying new watershed thresholds. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/SkullStripFix Hope that helps. -Louis On Tue, 2 Oct 2012, Rashmi Singh wrote: > 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 > > > _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
