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