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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