THanks for the response, Doug! So just to clarify, when I use mri_binarize with the 24 label, which indicates CSF, I shouldn’t expect to see any CSF in my mask other than that within ventricles? The reason I ask is I’m trying to generate the mask from which to acquire my csf regressor. Would you instead recommend using fslmaths or 3Dseg for that? How do FSL users typically go about it? I suppose I could do a subtraction of GM/WM masks from whole brain masks with a 3dcalc function. Just curious of the most common freesurfer method of acquiring csf regressors. Thanks!

On Sat, Nov 25, 2017 at 7:28 PM Douglas Greve <greve@nmr.mgh.harvard.edu> wrote:

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.77@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

--

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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