We do not currently segment extra cerebral CSF. We will have this
segmentation in the next version.
On 11/21/17 9:00 AM, Sam D wrote:
Hello again FS experts,
Has anyone encounter this issue with FS CSF masks I described below?
I’ve reposted the issue here. I appreciate the help!
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
/
/
On Fri, Nov 17, 2017 at 5:42 PM Sam D <dewitt...@gmail.com
<mailto:dewitt...@gmail.com>> wrote:
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 <tel:%28212%29%20241-0893>/
--
/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/
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