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There is one issue with this approach. When you apply the Affine matrix to the mat filed of header, the resulting matrix has a shear component. This inhibits the use of ROI analyses with DARTEL data. Does anyone know how to eliminate the shear components when apply the Affine matrix to the mat field of the header? Can the mat fields be rounded to 3 decimal places???? Any suggestions would be appreciated. On Wed, May 21, 2008 at 1:40 PM, Carlton Chu <[log in to unmask]> wrote: > Hi Naroa: > > If you leave NaN in the bounding box option, you should have exactly the > same dimensions as your native space. > Initial import only roates and translates the image in the native space, I > won't resize the brain. (ridge algnment) > > If you want to project your DARTEL warped brain into MNI space, you can > affine reigster your DARTEL template to the MNI template (use normalization > in SPM5, but set the iteration of non-linear warping to 0). Then you can > apply the Affine matrix M in the parameter file generated to each of your > dartel warped and modulated images before your statistical analysis. > (multiply the transformation matrix to the .mat field in the header of each > images). > > Then things will all work out. I believe John sent the script to apply the > transformation in the email list a while ago...you can search for it > > Carlton > > > > NAROA IBARRETXE BILBAO wrote: > > Hi, >> >> I have a very basic question. I have just started to use Dartel tool. >> >> During "initial import" step I do define bounding box instead of using >> NaN. I >> put the following parameters: -90 -126 -72; 90 90 108 because leaving NaN >> by >> default the brain resulted smaller than normal. >> >> But now I don't know if it is the right decision. Should I conserve the >> original >> parameters? >> >> If I have changed the bounding box parameter, when I apply deformations to >> convert the average to MNI space should I put the same parameters used >> before? >> >> Thank you >> ------------------------------------------------- >> This mail sent through IMP: http://horde.org/imp/ >> >> >> >> >> > -- Best Regards, Donald McLaren ===================== D.G. McLaren University of Wisconsin - Madison Neuroscience Training Program Tel: (773) 406 2464 ===================== 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 (773) 406 2464 or email.