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