Re: [Freesurfer] Segmentation problem recon-all

I see. Yes, that kind of thing is hard. YOu can try the gcuts skullstripping, which is more aggressive and can sometimes get rid of this kind of thing, but it also is more likely to strip brain. Or manually remove those voxels in the brainmask.mgz

cheers Bruce On Thu, 22 Jun 2017, Lisa Delalande wrote:

Hi Bruce,

Thank you very much for your mail. I am going to specify my question.

In fact, we saw a problem after the recon-all step. The dura was included in the lh.pial and rh.pial. Indeed, the red demarcation included the meninges.

I send you an attachment

Cheers

Marine

2017-06-21 18:51 GMT+02:00 Bruce Fischl fischl@nmr.mgh.harvard.edu: Hi Marine

  the brainmask is just a rough estimate of what is brain and what
  is not. You don't need to worry if it is not accurate *unless*
  the lh.pial and/or rh.pial surfaces end up not being accurate
  because of dura left in the brainmask.

  cheers
  Bruce
  On Wed, 21 Jun 2017, Lisa Delalande wrote:


        Hi,

         

        I am a PhD student and faced a problem with
        Freesurfer, more specially with
        segmentation. First of all, I did a typical qsub
        command. However, when I
        cheked with tkmedit, I saw problems of brainsmask.
        Indeed, meninges are
        often considered as grey matter.

        I tried these different commands :


        1.) setenv SUBJECTS_DIR /path/to/your/data

        setenv WATERSHED_PREFLOOD_HEIGHTS '20 30 40 50'

        recon-all -multistrip -clean-bm -s <subjid>
        -no-isrunning


        2.) recon-all -skullstrip -clean-bm -gcut -subjid
        <subjid>

        cd $SUBJECTS_DIR/yoursubj/mri/transforms

        cp talairach_with_skull.lta bak

        cp talairach_with_skull_2.lta
        talairach_with_skull.lta

        recon-all -s yoursubj -skullstrip -clean-bm
        -clean-lta"

         

        without success I finally used a manual method :

         

        3.) tkmedit skullstrip3_before brainmask.mgz -aux
        T1.mgz

         

        but the latter is source of error and
        time-consuming. I've got 105 MRI scans
        to rectify. Do you have a council to improve le
        first step of the reconn-all
        ?


        Sincerely
        Marine Moyon

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