That sounds great, of course! Is mris_volmask a new script? It doesn't seem to be present in my installation, which I downloaded last week. Where can I get that program?
When I fed a higher-resolution volume as template to mri_surf2vol with --fillribbon, it actually worked just fine, except for the same graininess bug mentioned. So if there's already a bug fix version of mri_surf2vol available I'd sure like to have it now so I can try it out. It is probably sufficient for my current needs.
Where can I get the new mri_surf2vol?
Thanks so much for your help...
On May 5, 2007, at 8:37 AM, Gheorghe Postelnicu wrote:
It can do that, although this is not supported currently.
Also, the current binary for the ribbon generation is called mris_volmask.
I think the best thing to do to satisfy your request is to introduce a new parameter for voxel scaling. This would be applied to the template voxel size (which is now by default orig.mgz).
How would that sound?
PS: this might take a couple of days, as I can foresee small technical problems occurring with the resolution increase.
On 5/5/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David,
there are two issues here. One is a known bug in which the ribbon isn't filled properly. This has been fixed by Gheorghe Postelnicu and Nick can post you a new version. The resolution is a different issue. Gheorghe: will your code handle generating higher resolution versions of the ribbon?
thanks, Bruce
On Sat, 5 May 2007, David Perlman wrote:
Is there a way to re-do the generation of the ribbon but
generate it with a
smaller voxel size? I've already had success resampling the
T1.mgz to 0.25mm
and using it as a template for mri_surf2vol with --mkmask and --
fillribbon,
but the problem is that only projects out from the vertices, so
the resulting
ribbon is sparse and thready, and doesn't fill the whole
cortical ribbon.
(Likewise the ?h.ribbon.mgz file seems to be missing a lot of
voxels in its
interior.)
Ideally what I want is to be able to overlay the surfaces onto a
volume of my
chosen resolution, and then fill the voxels between the
surface. I've been
looking at matlab code, and found this program: http://tinyurl.com/2bbyap surface2volume.m which allegedly does what I want, but it
doesn't actually
seem to work right when I try it: I get only a few scattered
voxels filled.
Does anyone have any idea of how to do this? Any help is greatly appreciated!
On May 3, 2007, at 10:31 AM, Bruce Fischl wrote:
Hi David,
we do generate such a thing called ?h.ribbon.mgz, but note that
once you go
back into the volume the topology is no longer preserved.
cheers, Bruce On Thu, 3 May 2007, David Perlman wrote:
I'm new to freesurfer, so I'm hoping this question isn't too
obvious.
I've searched the mailing list archives and the wiki but
haven't found any
leads.
I'm wondering if there's a way to generate a volume
representation of the
cortical sheet, based on the data from the white surface and
the pial
surface, so that the sheet will be guaranteed to have good
topology, as
well as retaining the proper thickness at each point? It
seems like all
the information for this is there already since we have the
two surfaces,
but I don't know how to go about figuring out how to convert
it into
volume data.
Here's a small image that might help give an idea of what I need: http://brainimaging.waisman.wisc.edu/~perlman/corticalsheet.png
In case you're curious, the reason I want this is because
we're trying to
test the novel method for cortical thickness measurement given in "Three-Dimensional Mapping of Cortical Thickness Using Laplace's Equation", Jones, Buchbinder and Aharon, Human Brain Mapping 11:12-32(2000).
--
dave----------------------------------------------------------------
After all, it is not *that* inexpressible. -H.H. The Dalai Lama
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
--
dave----------------------------------------------------------------
Science arose from poetry... when times change the two can meet
again
on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Gheorghe Postelnicu, PhD MGH, Harvard Medical School
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
On Sat, 2007-05-05 at 18:13 -0500, David Perlman wrote:
That sounds great, of course! Is mris_volmask a new script? It doesn't seem to be present in my installation, which I downloaded last week. Where can I get that program?
David,
You can get both of these here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist
get the files:
mri_surf2vol.gz
and
mris_volmask.tar.gz
to install mri_surf2vol, cp mri_surf2vol.gz to your $FREESURFER_HOME/bin, then type:
cd $FREESURFER_HOME/bin gunzip mri_surf2vol.gz chmod a+x mri_surf2vol
to install mris_volmask, cp mris_volmask.tar.gz to your $FREESURFER_HOME (notice this time its not the bin directory) then type:
cd $FREESURFER_HOME gunzip mris_volmask.tar.gz cd bin chmod a+x mris_volmask mris_volmask.bin vtk_setup
mris_volmask might not work because it requires the VTK libraries, which are not included in the publicly distributed freesurfer, but which i've included in the mris_volmask.tar.gz file.
Nick
On Sat, 2007-05-05 at 18:13 -0500, David Perlman wrote:
That sounds great, of course! Is mris_volmask a new script? It doesn't seem to be present in my installation, which I downloaded last week. Where can I get that program?
When I fed a higher-resolution volume as template to mri_surf2vol with --fillribbon, it actually worked just fine, except for the same graininess bug mentioned. So if there's already a bug fix version of mri_surf2vol available I'd sure like to have it now so I can try it out. It is probably sufficient for my current needs.
Where can I get the new mri_surf2vol?
Thanks so much for your help...
On May 5, 2007, at 8:37 AM, Gheorghe Postelnicu wrote:
It can do that, although this is not supported currently.
Also, the current binary for the ribbon generation is called mris_volmask.
I think the best thing to do to satisfy your request is to introduce a new parameter for voxel scaling. This would be applied to the template voxel size (which is now by default orig.mgz).
How would that sound?
PS: this might take a couple of days, as I can foresee small technical problems occurring with the resolution increase.
On 5/5/07, Bruce Fischl fischl@nmr.mgh.harvard.edu wrote:
Hi David,
there are two issues here. One is a known bug in which the ribbon isn't filled properly. This has been fixed by Gheorghe Postelnicu and Nick can post you a new version. The resolution is a different issue. Gheorghe: will your code handle generating higher resolution versions of the ribbon?
thanks, Bruce
On Sat, 5 May 2007, David Perlman wrote:
Is there a way to re-do the generation of the ribbon but
generate it with a
smaller voxel size? I've already had success resampling the
T1.mgz to 0.25mm
and using it as a template for mri_surf2vol with --mkmask and --
fillribbon,
but the problem is that only projects out from the vertices, so
the resulting
ribbon is sparse and thready, and doesn't fill the whole
cortical ribbon.
(Likewise the ?h.ribbon.mgz file seems to be missing a lot of
voxels in its
interior.)
Ideally what I want is to be able to overlay the surfaces onto a
volume of my
chosen resolution, and then fill the voxels between the
surface. I've been
looking at matlab code, and found this program: http://tinyurl.com/2bbyap surface2volume.m which allegedly does what I want, but it
doesn't actually
seem to work right when I try it: I get only a few scattered
voxels filled.
Does anyone have any idea of how to do this? Any help is greatly appreciated!
On May 3, 2007, at 10:31 AM, Bruce Fischl wrote:
Hi David,
we do generate such a thing called ?h.ribbon.mgz, but note that
once you go
back into the volume the topology is no longer preserved.
cheers, Bruce On Thu, 3 May 2007, David Perlman wrote:
I'm new to freesurfer, so I'm hoping this question isn't too
obvious.
I've searched the mailing list archives and the wiki but
haven't found any
leads.
I'm wondering if there's a way to generate a volume
representation of the
cortical sheet, based on the data from the white surface and
the pial
surface, so that the sheet will be guaranteed to have good
topology, as
well as retaining the proper thickness at each point? It
seems like all
the information for this is there already since we have the
two surfaces,
but I don't know how to go about figuring out how to convert
it into
volume data.
Here's a small image that might help give an idea of what I need: http://brainimaging.waisman.wisc.edu/~perlman/corticalsheet.png
In case you're curious, the reason I want this is because
we're trying to
test the novel method for cortical thickness measurement given in "Three-Dimensional Mapping of Cortical Thickness Using Laplace's Equation", Jones, Buchbinder and Aharon, Human Brain Mapping 11:12-32(2000).
--
dave----------------------------------------------------------------
After all, it is not *that* inexpressible. -H.H. The Dalai Lama
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
--
dave----------------------------------------------------------------
Science arose from poetry... when times change the two can meet
again
on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
-- Gheorghe Postelnicu, PhD MGH, Harvard Medical School
-- -dave---------------------------------------------------------------- Science arose from poetry... when times change the two can meet again on a higher level as friends. -Göthe
Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
freesurfer@nmr.mgh.harvard.edu
-
David Perlman -
Nick Schmansky