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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