The transforms list in the paper are volumetric transformation matrices. The wording was a little confusing in retrospective, but had to do with the goal of the transformation.
We decided that trying to create a surface from the 112RM-SL average itself wouldn't be an ideal way to create a surface for mapping macaque data. Our solution, at least for the foreseeable future, was to transform our average volume (112RM-SL) to the F99 volume. Since the surface is already aligned with the F99 volume, then essentially, the transform becomes an intermediate step in surface mapping. Specifically, apply the transform and then map the data to the surface. Hope that helps. Let me know if there are any other questions or interest in creating a surface for the 112RM-SL brain. Best Regards, Donald McLaren ================= D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Office: (608) 520-0586 ===================== This e-mail contains CONFIDENTIAL INFORMATION which may contain PROTECTED HEALTHCARE INFORMATION and may also be LEGALLY PRIVILEGED and which is intended only for the use of the individual or entity named above. If the reader of the e-mail is not the intended recipient or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that you are in possession of confidential and privileged information. Any unauthorized use, disclosure, copying or the taking of any action in reliance on the contents of this information is strictly prohibited and may be unlawful. If you have received this e-mail unintentionally, please immediately notify the sender via telephone at (608) 520-0586 or email. On Mon, Jul 5, 2010 at 8:03 AM, Figa Pelosa <[email protected]> wrote: > > > --- Ven 2/7/10, Donna Dierker <[email protected]> ha scritto: > > > Da: Donna Dierker <[email protected]> > > Oggetto: Re: [caret-users] 112RM to F99 Volume transformation > > A: "Caret, SureFit, and SuMS software users" < > [email protected]> > > Data: Venerdì 2 luglio 2010, 14:56 > > Hi R. Matt, > > > > I forwarded this message to Donald McLaren, but haven't > > heard from him. > > > > Meanwhile, I found this excerpt from an email from Donald > > to David Van > > Essen on January, 11, 2010: > > > > > The transform between the 112RM-SL and D99 is > > non-existent because we > > > took our 112RM average atlas and aligned it to the D99 > > brain to create > > > the 112RM-SL atlas. I have enclosed the > > final_ave_reg.mat (the > > > transform) and final_ave_reg.mat.prm (the breakdown of > > the rotation, > > > scale, translation, and skew parameters). This will be > > the closest > > > transform to the 112RM-SL to F99 that we have. > > [snip] > > > > > > The process used in the paper was to first align all > > the monkeys to an > > > average template (transforms are in the tar file) and > > to apply the > > > average to D99 transform to those images (final_ave > > transform) to get > > > them into the same space as the D99 brain. > > > > > > Thus, the average brain (not 112RM-SL) probably > > provides a better > > > estimate of average brain size. > > Here are the contents of the final_ave_reg.mat file: > > > > > 0.999876 0.00278264 -0.00811084 0.401485 > > > -0.00499908 1.00021 -0.0017622 0.452767 > > > 0.00604446 0.00073843 0.999452 -0.36121 > > > 0 0 0 1 > > Donna > > > > On 07/01/2010 12:37 PM, R. Matthew Hutchison wrote: > > > Hi all, > > > > > > This is a question directed at Dr. McLaren or anyone > > that regularly > > > works with the 112RM/F99 templates. > > > > > > Do you have a transformation matrix to normalize the > > 112RM volume to > > > the F99 volume? > > > > > > In the paper McLaren et al., 2009 there is a surface > > transformation, > > > but nothing for the volume. > > > > > > I was able to find a 112RM to F99 volume but with no > > transformation > > > matrix that I could invert. > > > > > > Thank you for any help. > > > > > > R. Matt > > > > > > > > > > _______________________________________________ > > 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 >
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