Hello,

I am attempting to generate a CSF mask from my aparc+aseg.nii image file.  However, my mask seems to only encompass the ventricular system itself, ignoring any other CSF (see attached image). I attempted to make the mask  using the following MRI_binarize command with FS labels.

 mri_binarize --i aparc+aseg.nii --match 4, 5, 14, 15 24, 31, 43, 44, 63, 122, 221, 257 --o CSF_test.nii

The labels corresponded to the structures listed below, including label 24, CSF. I assumed this would capture non-ventricular CSF.  Has anyone else encountered this issue? Any help would be greatly appreciated! 

4   Left-Lateral-Ventricle                  120 18  134 0

5   Left-Inf-Lat-Vent                       196 58  250 0

14  3rd-Ventricle                           204 182 142 0

15  4th-Ventricle                           42  204 164 0

24  CSF                                     60  60  60  0

31  Left-choroid-plexus                     0   200 200 0

43  Right-Lateral-Ventricle                 120 18  134 0

44  Right-Inf-Lat-Vent                      196 58  250 0

63  Right-choroid-plexus                    0   200 221 0

122 CSF-SA                                  74  255 74  0

221 Inf_Lat_Vent                            197 58  250 0

257 CSF-ExtraCerebral                      60  60  60  0

Sam DeWitt, Ph.D.
Postdoctoral Fellow
Pediatric Mood and Anxiety Disorders Program
Department of Psychiatry
Icahn School of Medicine at Mount Sinai
1240 Park Avenue, New York, NY 10029
Tel: (212)241-0893