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unsubscribe Rowena Handley Psychological Medicine TEL: 0207 848 0599 -----Original Message----- From: SPM (Statistical Parametric Mapping) [mailto:[log in to unmask]] On Behalf Of John Ashburner Sent: 02 June 2008 15:09 To: [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