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 FellowPediatric Mood and Anxiety Disorders ProgramDepartment of PsychiatryIcahn School of Medicine at Mount Sinai1240 Park Avenue, New York, NY 10029Tel: (212)241-0893 <(212)%20241-0893>*
