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Differences in smoothness is probably just due to differences in interpolation. VTK provides flat, phong and gouraud shading. These govern how the surfaces normals are calculated/interpolated between points, which are what is used for rendering lighting effects. Cheers, Brian > Dear Hanjian, > > This is actually not my personal mailbox - it is the FSL list. > I have been away from work for a few days. > Also, I am not familiar with other packages for displaying vtk files > and I > do not know if there is a strict standard as to which orientation (for > the left-right handedness) they are normally displayed. We display > things consistently with FSLView, which involves flipping left-right > for "neurologically ordered" files (positive determinant of the qform > or sform matrix). Our vtk coordinates use an internal coordinate > convention and do not follow the nifti conventions. Hence I am not > surprised that you see a left-right flip given these two significant > conventions (coordinates and display in FSLView). So I would > not worry about this. > > The arrows show the direction of the mean change between > groups. If they are tangential to the surface then the change > is along the surface and neither inward nor outward. > > I would not use fslswapdim to correct registration *errors*! > It is appropriate to use fslswapdim on your original images > to either fix labelling problems (A-P,L-R,S-I) or to put the images > in a more familiar orientation (like the standard templates). > However, I would *NOT* run it *after* any analysis has been > done. If you have a registration error then you should try to > fix it by cropping the image to remove large amounts of neck, > checking the brain extraction, changing the search space or > even selecting a different cost function. > > I hope this helps. > All the best, > Mark > > > > > On 4 Dec 2009, at 06:22, duhanjian wrote: > >> Dear Mark, >> I am very sorry to mail this letter to you mailbox directly. >> Beacause I haved sent those questions to the FSL mail box several >> days ago, but nobody answer those questions. So I mail those >> questions to you. Could you do me a favour? >> I was confused by following the questions. >> 1.Using FIRST package, I tried to make group analysis in patients vs >> normal controls. I found there was group difference in left >> amygdala and other structures. I tried to visualize the difference >> using vtk by my self. In the uploaded figure, I showed the left >> amygdala using vtk and fslview respectively. To my surprise, they >> are different. It seems to me that my result is a mirror image of >> the result obtained using fslview. In addition, the result obtained >> using fslview is smoother. Since I loaded the same >> NS_L_Amyg1_Fthresh.vtk file, why are the different in that way? >> >> 2.In addition, there are arrows which are tangent to the surface but >> the arrow is still outside the surface or inside the surface.Can we >> say that it is atrophy if the arrow lies inside the surface, no >> matter it is pointing inward or tangent to >> the surface? >> >> 3.In order to correct registration errors, I used fslswapdim >> command. What is the effect of fslswapdim? Should I take any >> additional steps when making group analysis if I performed the >> fslswapdim command? >> >> By the way, I have uploaded the pictures to >> http://www.fmrib.ox.ac.uk/cgi-bin/upload.cgi >> . The six-digit reference number for this upload session is 555243. >> >> Thank you very much! Mark >> >> >> >> 2009-12-04 >> yours sincerely, >> hanjian du >> Department of Neurosurgery, Southwest Hospital, Chongqing 400038, >> China >> >> 重庆市西南医院神经外科 >> 杜寒剑 > >