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Do you have the latest updates installed. There were some issues with the original release of the code that normalises to MNI space. Other than that, I can't figure out what the cause of the problem could be. Best regards, -John On Mon, 2009-09-28 at 17:44 +0200, Haakon Engen wrote: > Dear Donald, > > That was my immediate thought as well. However, I've coregistered the > T1 image to the mean functional image (output from the Realign:Unwarp > module) for every subject. I have verified that the alignment between > the T1 and functional images is within acceptable parameters for the > standard Segment+ normalise procedure for all subjects, having already > performed 1st and 2nd level analyses that I am hoping to compare with > the DARTEL normalised data. > > Comparing the original T1, the Template, the flow field and the mean > functional image yields the following for the two subjects (out of 39) I > have used to test DARTEL as of yet. > > It seems like the normalisation procedure flips the EPI's for some, to > me, obscure reason. > > Would skull stripping the images help in any way? > > Best wishes, > h. > > > > On 28.09.2009 16:31, MCLAREN, Donald wrote: > > Looks like your EPI images are aligned to the T1 images in native space > > (orientation is different). Use check reg to see if the native space EPI > > is aligned to the native space. If not, then you will need to align them > > first and make sure the orientations are the same. > > > > On Mon, Sep 28, 2009 at 4:49 AM, Haakon Engen > > <[log in to unmask] <mailto:[log in to unmask]>> > > wrote: > > > > Dear SPM'ers, > > > > I'm running into some weirdness using DARTEL to normalise my > > functional images. I have followed the recommended processing > > pipeline in the manual, using the "New Segment" module to create > > preimported rc*.img files that I've fed into the "Create templates" > > module. > > > > After normalising the data the results don't look too good, as you > > can see from the attached images. The functional images are severely > > distorted, while the flow fields and template looks fine (albeit > > from my limited understand of what fine DARTEL output is). Can > > anyone help me figure out where I've messed up? > > > > Please let me know if you need any more information. > > > > Best wishes, > > h. > > > > > > > > > > -- > > Best Regards, Donald McLaren > > ===================== > > Support the Alzheimer's Association Memory Walk 2009 ~~~ > > Join the Wisconsin Alzheimer's Disease Research Center team or make a > > donation. > > http://madison.kintera.org/2009/donaldmclaren > > > > > > ================= > > D.G. McLaren > > University of Wisconsin - Madison > > Neuroscience Training Program > > Office: (608) 265-9672 > > Lab: (608) 256-1901 ext 12914 > > ===================== > > 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) 265-9672 or email. > -- John Ashburner <[log in to unmask]>