OK, now I see. At first, it wasn't clear to me that this registration process also changed the number of nodes.
Thanks! On Apr 13, 2011, at 7:19 AM, Donna Dierker wrote: > If you did followed the steps in Spherical Registration (page 46) of > that tutorial, then you should have results in the ATLAS_LEFT_HEM directory. > > But rather than using the colin target, use this atlas target dataset > (PALS_B12.LR): > > http://sumsdb.wustl.edu/sums/archivelist.do?archive_id=6057499 > > This has the 73730 standard mesh sphere. > > If you register your subject to this target, then you will have your > deformed surface in the extracted atlas target directory on the 73730 mesh. > > If you have Freesurfer surfaces, I suspect the pipeline will be the > shorter path to what you want. > > On 04/12/2011 05:06 PM, Colin Davey wrote: >> Thanks Donna! >> >> >>> http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf >>> >> >> >> I have gone through that tutorial, but it doesn't change the number of >> vertices of the mesh (unless I missed something). As you said, "changing the >> geometry doesn't change the mesh". >> >> I'm asking about the ability to *resample* meshes to 73,730 nodes. "Using a >> strategy introduced by Saad et al (2004), the various surface >> configurations...were resampled so that they were represented using the >> 73,730-node 'standard-mesh'..." (A PALS Atlas of Human Cerebral Cortex, Van >> Essen 2005). Was that in Caret, or was that done outside of Caret? >> >> I haven't gotten the Freesurfer process under control yet, and will no doubt >> have questions about that before long (some basic newbie ones no doubt). >> >> On Apr 12, 2011, at 2:41 PM, Donna Dierker wrote: >> >> >>>> Thanks for the reply! >>>> >>>> I was under the impression that inflating, flattening and registration >>>> didn't change the number of verteces in the mesh. That way, one can easily >>>> go from a point in the flat mesh to the corresponding point in the >>>> original space. (ie, if a vertex on the flatmap is vertex number 12,329, >>>> than one need only get the coordinates of the 12,329th vertex of the >>>> corresponding cortical mesh.) >>>> >>> Correct -- changing the geometry doesn't change the mesh. >>> >>> >>>> I couldn't find a tutorial that shows how to do the surface-based >>>> registration to an atlas such that it changes the number of vertices (for >>>> example to '74k'). >>>> >>> Look for the word "Registration" in the title, e.g.: >>> >>> http://brainvis.wustl.edu/wiki_linked_files/documentation/Caret_5.5_Tutorial_Segment.pdf >>> >>> But as I said earlier, if you use the pipeline, there is a command line >>> step near the end of the postborder.sh script that runs spherical >>> registration. Everything in preborder.sh and postborder.sh is leading up >>> to this final step. >>> >>> >>> >>>> On Apr 9, 2011, at 8:25 PM, David Van Essen wrote: >>>> >>>> >>>>> Colin, >>>>> >>>>> Segmentation produces a 'native mesh' whose exact node number cannot be >>>>> prespecified in Caret (or in other segmentation algorithms I know >>>>> about). >>>>> >>>>> The 73,730-node mesh ('74k' in our latest lingo) arises from >>>>> surface-based registration to an atlas - either the macaque F99 atlas (a >>>>> 74k_f99 mesh) or the human PALS-B12 atlas (a 74k_pals mesh) - using the >>>>> appropriate tutorial. >>>>> >>>>> David VE >>>>> >>>>> >>>>> On Apr 8, 2011, at 6:48 PM, Colin Davey wrote: >>>>> >>>>> >>>>>> Hi, >>>>>> >>>>>> How do you create a 73,730 standard-mesh with Caret? I assume you begin >>>>>> by going through segmentation, flattening and registration process from >>>>>> the tutorial of the same name. But then what? >>>>>> >>>>>> Cheers, >>>>>> - C >>>>>> >>>>>> *************************************** >>>>>> Colin Davey >>>>>> Scientist >>>>>> Senior Software Engineer >>>>>> >>>>>> Electrical Geodesics, Inc. >>>>>> 1600 Millrace Dr. St 307 >>>>>> Eugene, OR 97403 >>>>>> >>>>>> Learn Boogie Woogie Piano >>>>>> http://www.ColinDavey.com/BoogieWoogie >>>>>> *************************************** >>>>>> > > _______________________________________________ > caret-users mailing list > [email protected] > http://brainvis.wustl.edu/mailman/listinfo/caret-users _______________________________________________ caret-users mailing list [email protected] http://brainvis.wustl.edu/mailman/listinfo/caret-users
