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>*
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 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>*
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 mailto: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 <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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
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 <%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*
Freesurfer mailing listFreesurfer@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
If you just use 24, then you will see a small patch near cerebellum. The 257 is not part of the analysis yet. All the others are venticular
On 11/26/17 3:40 PM, Sam D wrote:
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 mailto: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 <mailto: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 <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/ _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer_______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.--
/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/
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
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Sam D