Hi Phtseng, You have drawn attention to a well-known deficit in SureFit: There is no quick, easy way to update the ERROR_CORRECTION_INTERMEDIATES/*errors*mnc file, from which the SURFACES/*errors*RGB_paint is generated. This is the same mnc file that is the default file selection when you press the Locate Objects button on the Interactive Error Correction tab.
This *errors*mnc file is generated only when you run automatic error correction, which is the most time-consuming portion of the Run SureFit routine. When vol2 is loaded (e.g., after you run segmentation and/or have been patching), then the defaults on the Run SureFit menu change to skip error correction and prepare to flatten. This is because typically one doesn't use the Run SureFit menu until you have patched all the handles and are ready to Prepare to Flatten. You can change the settings to Correct Errors and Review Surface First, but this will take a long time to run -- certainly not something you want to do after fixing each handle. Instead, learn to rely less on the Locate Objects output and the SURFACES/*errors*RGB_paint coloring on the surface, and just LOOK for the handles on the inflated surface. Usually, you can see them if you rotate the surface, zooming and panning as needed to get a close-up view of all areas. If you can't see the handles, then they're often not worth fixing. Is this the SureFit demo volume you are trying to patch? It doesn't have many handles. What is your handle count? If more than one or two, then perhaps your patching has introduced some handles. Learning to patch is certainly the hardest part of learning to use SureFit, and it is probably harder than flattening, registering, or mapping in Caret. If you like, I can have a look at your segmentation volume and help you figure out exactly what to do to fix the handles. If this is not the demo volume, or if you used cropping parameters (xmin, xmax, ymin, ymax, zmin, zmax values on the Define VOI tab during Volume Preparation) other than those specified in the tutorial, then I'll also need your *sMRI.mnc and *sMRI.params file. Upload these files here: http://pulvinar.wustl.edu/cgi-bin/upload.cgi Right now, both John Harwell and I are working on integrating Caret and SureFit. After SureFit's functions are merged into Caret, then we envision numerous improvements -- including making patching easier and more intuitive. Donna On 11/11/2004 02:27 AM, pohetsn wrote: > Dear all > > What I want to do is > 1. depressing "Run Surefit" > 2. draw segment errors on surface > 3. correcting some handle errors > 4. saving the new edit > 5. depressing "Run SureFit" again (default setting) > 6. checking the surface of lately fixed handle errors > 7. draw the other segment errors which I havn't fixed > > However, at step7, I can't find some file looks like > *.segment.errors.xxxxx.RGB_paint > except the one which generated at step 2. > > e.g. > I can find files as follows: > Test.L.occipital.segment_corr2.patch.38499.surface_shape > Test.L.occipital.segment_corr2.patch.38499.topo > Test.L.occipital.segment_corr2.patch.ellipsoid.38499.coord > Test.L.occipital.segment_corr2.patch.ellipsoid.38499.vtk > Test.L.occipital.segment_corr2.patch.fiducial.38499.coord > Test.L.occipital.segment_corr2.patch.fiducial.38499.vtk > Test.L.occipital.segment_corr2.patch.geography.38499.paint > Test.L.occipital.segment_corr2.patch.geography.38499.RGB_paint > Test.L.occipital.segment_corr2.patch.inflated.38499.coord > Test.L.occipital.segment_corr2.patch.inflated-50.38499.vtk > Test.L.occipital.segment_corr2.patch.raw.38499.coord > Test.L.occipital.segment_corr2.patch.raw.38499.vtk > Test.L.occipital.segment_corr2.patch.sulci.38499.RGB_paint > Test.L.occipital.segment_corr2.patch.Surface.38499.spec > > but I cannot find anything like > Test.L.occipital.segment_corr2.patch.errors.38499.RGB_paint > in the SURFACE folder. > > Anyway, how to do step.7? > It's important while having lots handle errors. > > thank you > > Sincerely, > phtseng > > > _______________________________________________ > caret-users mailing list > caret-users@brainvis.wustl.edu > http://pulvinar.wustl.edu/mailman/listinfo/caret-users >
