[caret-users] Reconstruct into surface command line

Hi, Does the caret have a command line function to reconstruct a surface from contours, equivalent to the GUI: Layers-Reconstruct into Surface? I can't seem to find it. Cheers, Tristan ___ caret-users mailing list caret-users@brainvis.wustl.edu

Re: [caret-users] Volume segmentation error: RadialPositionMap

-Inferior orientation and their stereotaxic coordinates must be set so that the origin is at the anterior commissure. On Jul 28, 2013, at 10:31 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: But doesn't this require you already have a surface? I'm trying

Re: [caret-users] Volume segmentation error: RadialPositionMap

NIFTI_GZIP (RECOMMENDED) SPM WUNIL On Jul 24, 2013, at 9:14 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: Hi, I am trying to create a surface from a segmentation volume using the command line. The anatomy volume was not segmented

[caret-users] Volume segmentation error: RadialPositionMap

Hi, I am trying to create a surface from a segmentation volume using the command line. The anatomy volume was not segmented with Caret. When I do this: caret_command -volume-segment seg.nii Other.Case.L.spec NNYYN 1 0 NN LEFT SUREFIT_THEN_GRAPH NIFTI_GZIP I get: VOLUME

Re: [caret-users] Body weight of the F99UA1 case

;22(10):2227-40. doi: 10.1093/cercor/bhr290. Epub 2011 Nov 2. PMID: 22052704 David On Jun 17, 2013, at 7:34 PM, Tristan Chaplin wrote: Hi, Does anyone know the weight of the F99UA1 macaque? I can't seem to find it anywhere. Thanks, Tristan

Re: [caret-users] Mirroring hemispheres and Landmark Vector Difference registration

of the problem. If not, let me know offline, as we might need to take a look at your dataset. David On Mar 23, 2012, at 1:15 AM, Tristan Chaplin wrote: Hi, I've been registering left hemispheres to a right hemispheres using the landmark pinned relaxation algorithm and getting reasonable results, so

[caret-users] Mirroring hemispheres and Landmark Vector Difference registration

Hi, I've been registering left hemispheres to a right hemispheres using the landmark pinned relaxation algorithm and getting reasonable results, so I presume process automatically mirrors hemispheres so they match. I wanted to try the new landmark vector difference algorithm. Using similar

[caret-users] Open vs closed borders for registration

Hi, I just wondering, is there advantage/disadvantage to using open or closed borders in registration? e.g. why is the medial wall two borders and not a single closed border? I had heard a while back that originally borders could only be drawn on flat surfaces so this must have been necessary

Re: [caret-users] marmoset

Colin, the person working on the marmoset atlas was me. My boss, Marcello Rosa, and his colleagues Paxinos, Watson, Petrides and Tokuna recently published an atlas in book form:

Re: [caret-users] Interspecies comparisons - creating a new atlas for a different primate species

sphere, or maybe just use the subject sphere and a new sphere to generate a deformation map, and deform the subject native surfaces to the new mesh (this is approximately what spec file change resolution does). Tim On Mon, Feb 20, 2012 at 6:55 PM, Tristan Chaplin tristan.chap...@gmail.com

Re: [caret-users] Interspecies comparisons - creating a new atlas for a different primate species

a regularly divided geodesic sphere, but it will give you something close). If all else fails, there are a few spheres in the caret data directory. Tim On Thu, Feb 16, 2012 at 6:56 PM, Tristan Chaplin tristan.chap...@gmail.com wrote: Hi, A while back I asked about creating standard mesh

[caret-users] Problems after flattening - clear temp files?

Hi, I've been using caret for a while but just started having some trouble with flattening, I'm hoping someone has a quick technical fix. I'm using OSX 10.6.7. After running the morphing, it displays the crossover and errors screen, but you can't click close, you have to force quit the process.

Re: [caret-users] Standard mesh of 73,730 nodes.

Ok thanks for the information. On Fri, Feb 4, 2011 at 03:25, Donna Dierker do...@brainvis.wustl.eduwrote: On 02/01/2011 07:31 PM, Tristan Chaplin wrote: Hi, I've been reading about the creation of your atlases, and I see that PALS and the macaque atlases have standard size mesh

[caret-users] Sulcal depth from histological slices without an MRI/atlas

Hi everyone, I've made a few models from histological slices and I was wondering if there is any way of calculating sulcal depth without an MRI volume or atlas. There aren't any MRIs for my animals and there aren't any atlases for this species. I understand the I need a cerebral hull, which is

Re: [caret-users] Calculating mid-thickness and accurately drawing borders

clean it up and redo it in C++ for Caret, but like you we have other priorities. Thanks, Tristan On Tue, Jan 18, 2011 at 16:24, David Van Essen vanes...@wustl.edu wrote: Tristan, On Jan 17, 2011, at 6:56 AM, Tristan Chaplin wrote: Hi, I'm working on constructing brain models from

[caret-users] Calculating mid-thickness and accurately drawing borders

Hi, I'm working on constructing brain models from histological sections with cortical areas demarcated. Until now we've been writing our own progrms to achieve this. I'd like to start to use Caret for more of this work so non-programmers can do it and our data is more compatible with other

Re: [caret-users] Importing VTK polygon CELL_DATA in Caret

Thanks I'll check that out. I can write a program to convert between two data formats if Caret has some appropriate file format. Something where you can assign data to the mesh polygons, so you can then say colour the surface in caret with that data, as you would if it was mean curvature etc. I

[caret-users] Importing VTK polygon CELL_DATA in Caret

Hi, I'm pretty new to Caret, so far I've just been using it for reconstruction from histological slices and flattening. I have some pre-existing VTK surface models in which the polygons have some data associated with them, e.g. number tracer labelled cells, visuotopic information etc. In the