Hi,

The surface isn't from an individual subject, but generated from MNI space itself. What exactly do you mean by sample it onto the surface? I could make an image file with value one at the coordinate of interest and zero elsewhere, and then overlay it on surface space and see where it lies, but it would be rather tedious to do this for each of the coordinates I'm interested in (about 30), so I'm wondering if there is a faster way. Granted, some of them may not lie on cortical surface.

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

Hi Ben,

any given MNI coordinate may or may not be on the surface of a subject. You can convert it to individual subject space then sample it onto the surface.

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

I'm wondering how to convert a single voxel coordinate in 2mm MNI152 space to a location on a cortical surface representation of MNI space generated by Freesurfer. My broader goal is to present a set of coordinates collected for a meta-analysis on surface space. Thanks,

Ben Deen Department of Psychology, Yale University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Hi,

I didn't generated the surface myself (a technician in my lab did), but I imagine it entailed the same process as for a subject, just using the MNI152 brain instead of a single individual's anatomical image. I'm hoping to find the location on this surface of several peak coordinates from past studies, so that I can present the results of an informal meta-analysis by drawing dots (or some such) at these locations on an image of the surface. Thanks,

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

Hi Ben,

I'm still confused. How do you get a surface from an MNI average? Or is it from the colin dataset? Can you tell us a bit more about what you are trying to do so we can see if we can help?

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

The surface isn't from an individual subject, but generated from MNI space itself. What exactly do you mean by sample it onto the surface? I could make an image file with value one at the coordinate of interest and zero elsewhere, and then overlay it on surface space and see where it lies, but it would be rather tedious to do this for each of the coordinates I'm interested in (about 30), so I'm wondering if there is a faster way. Granted, some of them may not lie on cortical surface.

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

any given MNI coordinate may or may not be on the surface of a subject. You can convert it to individual subject space then sample it onto the surface.

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

I'm wondering how to convert a single voxel coordinate in 2mm MNI152 space to a location on a cortical surface representation of MNI space generated by Freesurfer. My broader goal is to present a set of coordinates collected for a meta-analysis on surface space. Thanks,

Ben Deen Department of Psychology, Yale University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Ben might be using Oliver Lyttelton's mean MNI152 surface (i.e., the average of all 152 subjects' surfaces on the MNI mesh, as registered using CIVET).

On 09/09/2009 11:31 AM, Bruce Fischl wrote:

Hi Ben,

I would be pretty surprised if you can get a reasonable surface from the MNI152. I would have thought it was too blurry to distinguish many of the gyri from one another.

That said, if you do have one, you can make labels in the volume and sample them onto the surface with tksurfer by just loading them.

cheers, Bruce

On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

I didn't generated the surface myself (a technician in my lab did), but I imagine it entailed the same process as for a subject, just using the MNI152 brain instead of a single individual's anatomical image. I'm hoping to find the location on this surface of several peak coordinates from past studies, so that I can present the results of an informal meta-analysis by drawing dots (or some such) at these locations on an image of the surface. Thanks,

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

I'm still confused. How do you get a surface from an MNI average? Or is it from the colin dataset? Can you tell us a bit more about what you are trying to do so we can see if we can help?

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

The surface isn't from an individual subject, but generated from MNI space itself. What exactly do you mean by sample it onto the surface? I could make an image file with value one at the coordinate of interest and zero elsewhere, and then overlay it on surface space and see where it lies, but it would be rather tedious to do this for each of the coordinates I'm interested in (about 30), so I'm wondering if there is a faster way. Granted, some of them may not lie on cortical surface.

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

any given MNI coordinate may or may not be on the surface of a subject. You can convert it to individual subject space then sample it onto the surface.

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

I'm wondering how to convert a single voxel coordinate in 2mm MNI152 space to a location on a cortical surface representation of MNI space generated by Freesurfer. My broader goal is to present a set of coordinates collected for a meta-analysis on surface space. Thanks,

Ben Deen Department of Psychology, Yale University _______________________________________________ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://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

you could just draw dots in the middle of the activated region I guess On Thu, 10 Sep 2009 benjamin.deen@yale.edu wrote:

Hi,

The surface I got from MNI152 looks pretty good.

I had tried to do what you're describing--I made 3x3x3 voxel cubes around each peak coordinate in the volume, and then viewed this in tksurfer. I've attached two images of the results from this, which hopefully will be successfully sent to the mailing list (red areas are from studies of theory of mind, blue areas are from studies of biological motion perception, purple is overlap, and an activation from the present study is outlined in black; the purple and black parts were drawn by hand in Photoshop). You can also see the surface derived from MNI152 in these images. This is OK, but I don't really like how messy the maps look, which seems inevitable with this approach. Thus, I was wondering whether it would be possible to get the locations of each coordinate on surface space by some other means, and then simply hand-draw a dot at these locations, to present the meta-analysis results on an inflated surface but in a nicer-looking way. Cheers,

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

I would be pretty surprised if you can get a reasonable surface from the MNI152. I would have thought it was too blurry to distinguish many of the gyri from one another.

That said, if you do have one, you can make labels in the volume and sample them onto the surface with tksurfer by just loading them.

cheers, Bruce

On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

I didn't generated the surface myself (a technician in my lab did), but I imagine it entailed the same process as for a subject, just using the MNI152 brain instead of a single individual's anatomical image. I'm hoping to find the location on this surface of several peak coordinates from past studies, so that I can present the results of an informal meta-analysis by drawing dots (or some such) at these locations on an image of the surface. Thanks,

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

I'm still confused. How do you get a surface from an MNI average? Or is it from the colin dataset? Can you tell us a bit more about what you are trying to do so we can see if we can help?

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

...

Hi,

The surface isn't from an individual subject, but generated from MNI space itself. What exactly do you mean by sample it onto the surface? I could make an image file with value one at the coordinate of interest and zero elsewhere, and then overlay it on surface space and see where it lies, but it would be rather tedious to do this for each of the coordinates I'm interested in (about 30), so I'm wondering if there is a faster way. Granted, some of them may not lie on cortical surface.

Ben

Quoting Bruce Fischl fischl@nmr.mgh.harvard.edu:

...

Hi Ben,

any given MNI coordinate may or may not be on the surface of a subject. You can convert it to individual subject space then sample it onto the surface.

cheers, Bruce On Tue, 8 Sep 2009 benjamin.deen@yale.edu wrote:

> > Hi, > > I'm wondering how to convert a single voxel coordinate in 2mm MNI152 > space to a > location on a cortical surface representation of MNI space generated > by > Freesurfer. My broader goal is to present a set of coordinates > collected for a > meta-analysis on surface space. Thanks, > > Ben Deen > Department of Psychology, Yale University > _______________________________________________ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > >