> > > on the same topic: > I don't understand why DARTEL is initialized only with the rigid component > of the matrix stored in the _sn.mat and not with the affine transformation. > Could you clarify this point? > From some notes by John Ashburner, the idea is to do all the nonlinear warping with the DARTEL algorithm, so that all shape parameters are estimated in a similar way with the DARTEL algorithm. This is rather tidier, especially if the idea is then to analyze shapes using the DARTEL "flow fields". Best regards, Gemma > > > > Quoting "MCLAREN, Donald" <[log in to unmask]>: > > (1) The rc*.nii images are rigidly aligned (6 parameters) to the MNI >> template space. This is done by applying the rigid component of the >> transformation stored in the *_sn.mat files. >> (2) In theory, the c*.img will produce crisper segments after warping >> because they have one less resampling step in the data processing stream. >> I >> have not yet inspected the differences between using rc* and c* files, >> yet; >> but it is on my to do list. >> >> (3) Creating flow field steps should always use the rc* files. >> >> On Fri, Jul 24, 2009 at 7:50 PM, Neil Chatterjee <[log in to unmask]> >> wrote: >> >> Dear SPMers, >>> >>> I'm trying to understand the Initial Import step for DARTEL a little >>> better, and I'm hoping someone here can help me out. >>> >>> Compared to the gray matter from the segment algorithm (c1*.nii), the >>> imported segments (rc1*.nii) seem to be aligned slightly differently (see >>> attached "misalignment.png"). The DARTEL guide indicates that some sort >>> or >>> rigid tissue alignment is happening in the import step, so this isn't too >>> surprising, though I am kind of lost as to what is being aligned to what. >>> Are the tissue classes rigidly aligned to some sort of SPM template? >>> >>> Referring to the imported images, the DARTEL guide also says that "the >>> headers of these files encode two affine transform matrices, so DARTEL >>> tools >>> are still able to relate their orientations to those of the original >>> T1-weighted images". Am I then correct in understanding that the flow >>> fields map the transformation from the original space of the T1 images to >>> the group template? To test it out, I warped a set of T1 scans before >>> and >>> after coregistration to the rc1*.nii images (see "avg_anat.png" attached) >>> using flow fields (u_rc1*.nii) from the dartel imported GM segments >>> (rc1*.nii). anat.nii shows the mean of the warped original T1 images, >>> and >>> ranat.nii shows the mean of T1 images that had been coregistered to the >>> rc1*.nii images prior to warping (rc1*.nii = ref, c1*.nii = source, T1 = >>> other) . anat.nii looks much cleaner than ranat.nii, implying that flow >>> fields map from original space to group template space. >>> Am I to take it then, that when creating modulated GM segments for >>> t-tests, >>> I should use the original segments and NOT the segments from DARTEL's >>> initial import? Comparing averages of warped GM segments from before >>> (c1*.nii) and after (rc1*.nii) import, it looks like it's the c1*.nii >>> that >>> warp together better (see attached "avggray.png"). If so, then perhaps >>> there is a slight mistake in the DARTEL guide, which indicates that the >>> rc1*.nii files (not the c1*.nii) should be selected when running "Create >>> Warped". Or is it that "Create Warped" and the Deformations toolbox are >>> not >>> doing the same thing? >>> >>> Any clarification would be much appreciated. This is using an updated >>> SPM8 >>> on Matlab 2008b. >>> >>> Regards, >>> Neil >>> >>> Neil Chatterjee >>> Research Assistant >>> Stanford Systems Neuroscience and Pain Lab >>> [log in to unmask] >>> >>> >> >> >> -- >> Best Regards, Donald McLaren >> ===================== >> 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. >> >> -- Gemma C. Monté Rubio ____________________________________________ CIBERSAM Unitat de Recerca | Hospital Benito Menni CASM Telf.+ 34 93 6529999-ext. 493 | Fax.+ 34 93 6400268 [log in to unmask]