Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
Hi Chris
that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce
On Wed, 25 Jul 2012, Christopher Coello wrote:
Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
Hi Bruce,
Absolutely, the voxels I'm referring to are defined regarding their distance to the cortical ribbon (let's say within 5 mm) rather than by belonging to a specific tissue type. Using a distance criteria from the ribbon surface and collect only voxels within a certain distance (going outwards) could be one solution. Is that possible with some functions in Freesurfer ?
Chris
On 25.07.2012 15:50, Bruce Fischl wrote:
Hi Chris
that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce
On Wed, 25 Jul 2012, Christopher Coello wrote:
Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
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.
Hi Chris,
sure, we can compute distance-to-surface transforms and such, but I don't think we have any pre-packaged binaries that will do what you want, just a set of C functions
Bruce On Wed, 25 Jul 2012, Christopher Coello wrote:
Hi Bruce,
Absolutely, the voxels I'm referring to are defined regarding their distance to the cortical ribbon (let's say within 5 mm) rather than by belonging to a specific tissue type. Using a distance criteria from the ribbon surface and collect only voxels within a certain distance (going outwards) could be one solution. Is that possible with some functions in Freesurfer ?
Chris
On 25.07.2012 15:50, Bruce Fischl wrote:
Hi Chris
that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce
On Wed, 25 Jul 2012, Christopher Coello wrote:
Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
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.
Hi Bruce,
Thanks for the reply. I'm not really familiar with compiling C functions, I have been working all the time with Matlab. Always worth to ask : do you have such set of C functions in Matlab also ?
Christopher
On 25.07.2012 16:10, Bruce Fischl wrote:
Hi Chris,
sure, we can compute distance-to-surface transforms and such, but I don't think we have any pre-packaged binaries that will do what you want, just a set of C functions
Bruce On Wed, 25 Jul 2012, Christopher Coello wrote:
Hi Bruce,
Absolutely, the voxels I'm referring to are defined regarding their distance to the cortical ribbon (let's say within 5 mm) rather than by belonging to a specific tissue type. Using a distance criteria from the ribbon surface and collect only voxels within a certain distance (going outwards) could be one solution. Is that possible with some functions in Freesurfer ?
Chris
On 25.07.2012 15:50, Bruce Fischl wrote:
Hi Chris
that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce
On Wed, 25 Jul 2012, Christopher Coello wrote:
Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
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.
Hi Christopher
see if mris_distance_transform does what you want.
cheers Bruce On Thu, 26 Jul 2012, Christopher Coello wrote:
Hi Bruce,
Thanks for the reply. I'm not really familiar with compiling C functions, I have been working all the time with Matlab. Always worth to ask : do you have such set of C functions in Matlab also ?
Christopher
On 25.07.2012 16:10, Bruce Fischl wrote:
Hi Chris,
sure, we can compute distance-to-surface transforms and such, but I don't think we have any pre-packaged binaries that will do what you want, just a set of C functions
Bruce On Wed, 25 Jul 2012, Christopher Coello wrote:
Hi Bruce,
Absolutely, the voxels I'm referring to are defined regarding their distance to the cortical ribbon (let's say within 5 mm) rather than by belonging to a specific tissue type. Using a distance criteria from the ribbon surface and collect only voxels within a certain distance (going outwards) could be one solution. Is that possible with some functions in Freesurfer ?
Chris
On 25.07.2012 15:50, Bruce Fischl wrote:
Hi Chris
that's tough to do with only a T1 image as CSF and bone look the same. We don't have any ready-made tools for doing what you want, but you could probably get close with some rules. Sounds like the voxels you are referring to are CSF or dura given their proximity to brain cheers Bruce
On Wed, 25 Jul 2012, Christopher Coello wrote:
Dear Freesurfer users,
I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels.
Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned.
My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ?
Thanks a lot in advance,
Best,
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.
freesurfer@nmr.mgh.harvard.edu
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Bruce Fischl -
Christopher Coello