[Mristudio-users] AIR image dimensions/ Talairach WMPM/Eigen vector flipping/ROI Error

[sd]

Hi，
I just wonder that which subject should I submit for the LDDMM process？The initial images or the images after linear transformation？
Sandy

At 2011-12-13 23:32:47,"Bill Quinn" <billquinndme at yahoo.com> wrote:

Hi mri-studio users and programmers,

First of all, thank you for well written program and also your fantastic follow up service. If possible I would like to ask a couple of questions just to clarify some questions that I have about the basic workings.

1. In Diffeomap I perform Air Linear Registration in order to align my data with that of the Template (in my case I use the Talairach atlas). My images are 256*256*55 and I normalise it with the template of dimensions 192*192*136. How much does the difference in image size affect the accuracy and reliability of the subsequent analysis.
As an additional to ensure the best LDDMM result, is the contrast of the two images the most important in setting up the images before entering the LDDMM screen?


2. When I load the Talairach WMPM from diffeomap as an ROI the regions of interest are loaded as object 1,2 etc. Is it possible to get the name of each region of interest? When I perform the intensity measurements using the WMPM I get the a table listing a the same amount of parts as the objects i.e. in the case of Talairach 170. I then use the following paper to find what the abbreviations stand for:

Oishi et al, Atlas-based whole brain white matter analysis using large deformation diffeomorphic metric mapping: Application to normal elderly and Alzheimer’s disease participants
euroimage 2009 June ; 46(2): 486–499. (Appendix A part 4)

Is this the correct approach? Or is it the that the regions of interest in the ROI objects box contain these parts as can be seen when I choose the button under Atlas: WMPM of division of defined ROIs


3. When I load or create the tensor image file (.d file) in DIffeoMap I am asked if I want to flip the eigenvectors. If I save the file as eigenvectors being flipped when I created the file do I also have to flip them again while opening the file afterwards or do I assume they are now in the correct direction?

4. Finally, when I create an ROI in either DTIStudio or ROI editor I save it as a binary map. When I then try to reload it in the fibre tracking section I am informed that the "Image parameters in this file are not consistent with with current ones, continue?" When I select yes the ROI loads in the expected position. Is it a normal occurance to get an error even though I created the ROI in the same image during the same DTIStudio session?

If any of these questions have already been answered, please just point me to the appropiate link.

Thank you for you time,

Best Regards,

William Quinn
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