DARTEL is generally applied to cross-sectional studies, but it could be used
for inter-subject registration in longitudinal studies. I wasn't sure which
you were doing. Because you were concerned with large anatomical
differences, I thought you may be using HDW for inter-subject registration.
You could still use DARTEL for spatially normalising Jacobian determinant
fields obtained from the HDW though.
Best regards,
-John
On Monday 02 June 2008 16:56, Senjem, Matthew L. [RO IMAGNG] wrote:
> Hi John,
> Thanks for your helpful response. In the last week I have re-read Chapter
> 4 of the HBF book, and in so doing I had arrived at the same answer you
> gave for my first question - it would require a lot of additional coding.
> To answer your question, we are doing a "traditional" TBM analysis, e.g.
> compute the change oer time in each person, then use the DCT parameters
> from unified segmentation to bring them all into template space. I must
> admit that I am still pretty unfamiliar with DARTEL, would this type of
> analysis be possible in DARTEL, or is DARTEL primarily for cross-sectional
> inter subject analyses?
>
> Best regards,
> Matt
>
>
> Matthew L. Senjem
> Department of Information Technology
> Opus Center for Advanced Imaging Research
> Mayo Clinic, Rochester, MN, USA
> [log in to unmask]
> 507-538-0764 (office)
> 612-382-0396 (direct)
>
>
>
>
>
> -----Original Message-----
> From: John Ashburner [mailto:[log in to unmask]]
> Sent: Mon 6/2/2008 9:08 AM
> To: Senjem, Matthew L. [RO IMAGNG]; [log in to unmask]
> Subject: Re: [SPM] HDW question
>
> > I am wondering, in the HDW toolbox, is it possible to specify a mask
> > image over which the likelihood potentials are calculated?
>
> No. Not without quite a lot of additional coding.
>
> > Or does it even make
> > sense to do that? I am wondering if it is possible to constrain the
> > warping algorithm such that its cost function is calculated only in the
> > masked regions. I have noticed that in some images where there is
> > extremely bright dura near the brain, the presence of the dura in one
> > image but not the other seems to be driving the warping, i.e. the warping
> > field calculated over the brain voxels near this bit of dura seems to be
> > heavily influenced by the presence or absence of the dura. In other
> > words, we are finding large regions of "expansion" or "contraction" in
> > the brain voxels near the bright dura, but it seems to be a result of the
> > algorithm trying to match the dura between the two scans. I have tried
> > simply extracting the brain from both images, which seems to help in some
> > ways, but I believe it introduces artificial edges which have their own
> > unintended effects on the result. Sorry for the long winded explanation,
> > but is there a way to mask out certain voxels from the likelihood
> > potential calculation without introducing an artificial edge? Thanks for
> > any insight you can offer,
>
> I don't have any bright ideas that would help here. Are you doing
> inter-subject registration? If so, then you could try the DARTEL toolbox,
> which warps GM to GM and WM to WM.
>
> Best regards,
> -John
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