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 –s AA***.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.
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.
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" fischl@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.
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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" fischl@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.
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