Hi Allison,

Sorry if i was unclear, what i'm interested in is the WM. As you say the current WM surface provides good information in separating the WM from the Gm, I would also like to have a surface which separates the WM from the subcortical structures. Is this possible?

Could i for instance take the volume information in aseg.mgz generate surfaces of the subcortical structures then some how remove these areas from the overall WM surface.

Alternatively, if I had a WM volume mask, that didn't include the subcoritcal regions. ie by sorting through aseg.mgz. could I somehow generate a new surface the is the boundary of this mask?

Thanks for the help. Luke

On 12/22/2010 04:35 PM, Allison Stevens wrote:

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hello,

I'm new to freeSurfer and just starting to look around so I apologize if this question is a bit naive.

When I look at segmentation results, that include deep brain nuclei (thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented?

I imagine that this would change the topology of the WM region thus it might be difficult, Is there away to generate surfaces form these regions on there own?

Thanks Luke _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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I figured out that what i want to be calling is mri_tessellate but on a mask of the cortical WM. I can create this mask from aseg.mgz provided I know what the labels that i want extracted are.

Is there a file somewhere that says that 2 and 41 are the cortical WM. ideally I'd like to know all of the labels so that i won't have to bother people everytime i want to look at a different region.

Thanks. Luke

On 12/22/2010 05:10 PM, Allison Stevens wrote:

Oh, I see - the Total wm volume reported in the aseg.stats will not include these structures even though they look included by the surfaces. Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Allison,

Sorry if i was unclear, what i'm interested in is the WM. As you say the current WM surface provides good information in separating the WM from the Gm, I would also like to have a surface which separates the WM from the subcortical structures. Is this possible?

Could i for instance take the volume information in aseg.mgz generate surfaces of the subcortical structures then some how remove these areas from the overall WM surface.

Alternatively, if I had a WM volume mask, that didn't include the subcoritcal regions. ie by sorting through aseg.mgz. could I somehow generate a new surface the is the boundary of this mask?

Thanks for the help. Luke

On 12/22/2010 04:35 PM, Allison Stevens wrote:

...

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hello,

...

I'm new to freeSurfer and just starting to look around so I

apologize if

...

this question is a bit naive.

...

When I look at segmentation results, that include deep brain

nuclei

...

(thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented?

...

I imagine that this would change the topology of the WM region

thus it

...

might be difficult, Is there away to generate surfaces form these regions on there own?

...

Thanks

Luke _______________________________________________ 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.

Hi Bruce,

Basically what i would like to do is to generate a surface for the cerebral Wm. additionally I would like to label each vertex based on the anatomy on the other side of the boundary. This is mostly for a visualization but might be useful in other contexts.

My strategy is to extract the right and left cerebral WM as well as the corpus callosum from the aseg result using the FreeSurferColorLUT.txt to tell me the labels to extract. This i will most likely do in fslmaths or with afni as I am more familar with them. If a freesurfer cmd is available that would certainly work as well.

Using this mask I'll compute a surface using either mri_mc or mri_tessellate. what is the difference by the way?

Then I'll compute the surface normals at each vertex and based on those label each vertex.

I'm certainly open to any suggestions on how to make this simpler. or perhaps such a tool already exists in FS. Thanks, Luke

On 12/22/2010 10:06 PM, Bruce Fischl wrote:

Hi Luke,

you could, but perhaps it would be easier if you explained what your bigger goal is?

cheers, Bruce On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Allison,

Sorry if i was unclear, what i'm interested in is the WM. As you say the current WM surface provides good information in separating the WM from the Gm, I would also like to have a surface which separates the WM from the subcortical structures. Is this possible?

Could i for instance take the volume information in aseg.mgz generate surfaces of the subcortical structures then some how remove these areas from the overall WM surface.

Alternatively, if I had a WM volume mask, that didn't include the subcoritcal regions. ie by sorting through aseg.mgz. could I somehow generate a new surface the is the boundary of this mask?

Thanks for the help. Luke

On 12/22/2010 04:35 PM, Allison Stevens wrote:

...

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hello,

I'm new to freeSurfer and just starting to look around so I apologize if this question is a bit naive.

When I look at segmentation results, that include deep brain nuclei (thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented?

I imagine that this would change the topology of the WM region thus it might be difficult, Is there away to generate surfaces form these regions on there own?

Thanks Luke _______________________________________________ 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.

---

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Thanks, Can i supply multiple labels to combine into a single surface, (e.g. both 2 and 41). From the usage it seems that connectivity might be what i want but i'm not sure I understand the syntax. would i call it

mri_mc $PATHTOASEC 2 CereWM 2=42?

USAGE: mri_mc input_volume label_value output_surface [connectivity] option connectivity: 1=6+,2=18,3=6,4=26 (default=1)

thanks Luke

On 12/22/2010 10:45 PM, Bruce Fischl wrote:

Hi Luke,

mri_mc is newer and more flexible, and also implements marching cubes. You don't need to extract any labels from the volume, as mri_mc explicitly takes a label to cover the surface of (e.g. 2 or 41).

cheers Bruce

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Bruce,

Basically what i would like to do is to generate a surface for the cerebral Wm. additionally I would like to label each vertex based on the anatomy on the other side of the boundary. This is mostly for a visualization but might be useful in other contexts.

My strategy is to extract the right and left cerebral WM as well as the corpus callosum from the aseg result using the FreeSurferColorLUT.txt to tell me the labels to extract. This i will most likely do in fslmaths or with afni as I am more familar with them. If a freesurfer cmd is available that would certainly work as well.

Using this mask I'll compute a surface using either mri_mc or mri_tessellate. what is the difference by the way?

Then I'll compute the surface normals at each vertex and based on those label each vertex.

I'm certainly open to any suggestions on how to make this simpler. or perhaps such a tool already exists in FS. Thanks, Luke

On 12/22/2010 10:06 PM, Bruce Fischl wrote:

...

Hi Luke,

you could, but perhaps it would be easier if you explained what your bigger goal is?

cheers, Bruce On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Allison,

Sorry if i was unclear, what i'm interested in is the WM. As you say the current WM surface provides good information in separating the WM from the Gm, I would also like to have a surface which separates the WM from the subcortical structures. Is this possible?

Could i for instance take the volume information in aseg.mgz generate surfaces of the subcortical structures then some how remove these areas from the overall WM surface.

Alternatively, if I had a WM volume mask, that didn't include the subcoritcal regions. ie by sorting through aseg.mgz. could I somehow generate a new surface the is the boundary of this mask?

Thanks for the help. Luke

On 12/22/2010 04:35 PM, Allison Stevens wrote:

...

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hello,

I'm new to freeSurfer and just starting to look around so I apologize if this question is a bit naive.

When I look at segmentation results, that include deep brain nuclei (thalamus etc) I see that they are all contained inside of the white matter surface. is there away to edit the surface so that these boundaries are represented?

I imagine that this would change the topology of the WM region thus it might be difficult, Is there away to generate surfaces form these regions on there own?

Thanks Luke _______________________________________________ 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.

---

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Hi Luke surf2surf using sphere.reg uses the surface based registration isn't what you want. CVS should work, but I'm not sure Lilla has written anything to apply is to a surface. You could apply it to your volume mask then tessellate that I guess Bruce

On Dec 23, 2010, at 10:13 AM, Luke Bloy luke.bloy@gmail.com wrote:

So I hit a snag...

I can extract the ROIs that I want and combine them into a single binary mask( allWM.mgz ). I can then run mri_mc on that mask like this.

mri_mc allWM.mgz 1 AllWhite

this generates a surface lh.AllWhite which i then move to the subjects surf directory. I can view the surface and it looks ok.

However I'm not sure why it uses the lh prefix to specify a hemisphere but thats is ok since I need it to run mri_surf2surf to generate the normals. Here is where i run into problems.

mri_surf2surf --s sub1 --hemi lh --sval-nxyz AllWhite --tval lh.AllWhite.normX --tfmt w --frame 0

this finds my surface file but fails with the following message.

Reading source surface reg /home/lbloy/data/freeSurfer//sub1/surf/lh.sphere.reg Loading source data Reading surface file /home/lbloy/data/freeSurfer//sub1/surf/lh.AllWhite Extracting surface normals INFO: surfcluster: NOT fixing group surface area INFO: trgsubject = srcsubject Saving target data Saving as paint format ERROR: MRIScopyMRI: Surf/Src dimension mismatch. Warning: all vertex values are zero

I suspect that the problem is the comparison of the lh.AllWhite surface to lh.sphere.reg

I've tried not specifying a hemisphere but that doesn't work. Are there additional steps i need to do before i can run mri_surf2surf an inflation or topology correction perhaps.

I appreciate any help since I understand that i'm trying to do things that the tools weren't really intended to do. Thanks again Luke

On 12/22/2010 10:45 PM, Bruce Fischl wrote:

...

Hi Luke,

mri_mc is newer and more flexible, and also implements marching cubes. You don't need to extract any labels from the volume, as mri_mc explicitly takes a label to cover the surface of (e.g. 2 or 41).

cheers Bruce

On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Bruce,

Basically what i would like to do is to generate a surface for the cerebral Wm. additionally I would like to label each vertex based on the anatomy on the other side of the boundary. This is mostly for a visualization but might be useful in other contexts.

My strategy is to extract the right and left cerebral WM as well as the corpus callosum from the aseg result using the FreeSurferColorLUT.txt to tell me the labels to extract. This i will most likely do in fslmaths or with afni as I am more familar with them. If a freesurfer cmd is available that would certainly work as well.

Using this mask I'll compute a surface using either mri_mc or mri_tessellate. what is the difference by the way?

Then I'll compute the surface normals at each vertex and based on those label each vertex.

I'm certainly open to any suggestions on how to make this simpler. or perhaps such a tool already exists in FS. Thanks, Luke

On 12/22/2010 10:06 PM, Bruce Fischl wrote:

...

Hi Luke,

you could, but perhaps it would be easier if you explained what your bigger goal is?

cheers, Bruce On Wed, 22 Dec 2010, Luke Bloy wrote:

...

Hi Allison,

Sorry if i was unclear, what i'm interested in is the WM. As you say the current WM surface provides good information in separating the WM from the Gm, I would also like to have a surface which separates the WM from the subcortical structures. Is this possible?

Could i for instance take the volume information in aseg.mgz generate surfaces of the subcortical structures then some how remove these areas from the overall WM surface.

Alternatively, if I had a WM volume mask, that didn't include the subcoritcal regions. ie by sorting through aseg.mgz. could I somehow generate a new surface the is the boundary of this mask?

Thanks for the help. Luke

On 12/22/2010 04:35 PM, Allison Stevens wrote:

...

Hi Luke, For subcortical structures, you would want to use the volume information provided by the aseg.mgz and not information from the surfaces (which are intended for cortical measures). Allison

On Wed, 22 Dec 2010, Luke Bloy wrote:

> Hello, > > I'm new to freeSurfer and just starting to look around so I apologize if > this question is a bit naive. > > When I look at segmentation results, that include deep brain nuclei > (thalamus etc) I see that they are all contained inside of the white > matter surface. is there away to edit the surface so that these > boundaries are represented? > > I imagine that this would change the topology of the WM region thus it > might be difficult, Is there away to generate surfaces form these > regions on there own? > > Thanks > Luke > _______________________________________________ > 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.

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