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 <fis...@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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