 |
 |
Sometimes there is a bit too much extra information in the anatomical scans, which can confuse the (normalised) mutual information coregistration. Here is a recycled response ( https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0906&L=SPM&P=R49092 ), which may help. Probably the easiest fix for this would be to use the Segment button (maybe the New Segment of SPM8) to generate native space tissue class images of GM, WM and CSF, as well as a bias corrected version of your anatomical scan. The c1, c2 and c3 images could be used to skull strip the bias corrected anatomical scan, which should give you an image that coregisters rather better. The skull stripping bit can be done using ImCalc, where you would select the m***.img, c1***.img, c2***.img and c3***.img. The expression to evaluate would then be i1.*((i2+i3+i4)>0.5) . If you plan to use the ***_seg_sn.mat file for spatially normalising, then you should coregister the functional data to the output of ImCalc. This would be done by having the ImCalc result as "reference", one of the fMRI scans as the "source", and all the others as "other". Best regards, -John On 8 November 2010 09:48, Brian Murphy <[log in to unmask]> wrote: > Hi, > > I have one participant session that will not coregister for me correctly. I > am using the same preprocessing procedure as worked well on two previous > participants, so I don't think there is an error in the script. > > The result I am getting is that the structural image is rolled a little to > the left (~0.05 rad), pitched forward (~.1-.2 rad) and displaced downwards. > Functional realignment is working fine, and I am using the resulting mean > image as the reference. > > The things I have tried so far are to make the tolerances smaller, to move > the origin in the structural image on to the AC (using the Display > function), to approximately align the functional and structural images by > hand (with Check Reg), and combinations of these. But always when I re-run > coregistration I get the same result. > > I guess it might have something to do with my functional scanning parameters > - I'm scanning broad coverage of cortex (just missing a bit of motor and > temporal) on a short TR (1s) and coarse resolution (3x3x5mm). Is it > generally difficult to get such low resolution, low contrast images to > coregister correctly? > > (BTW on this third participant, I'm using dummy scans. On the previous two > that coregistered well, I did record the initial high-contrast scans. Since > I am using the mean of ~400 functional images as reference, I guess those > few initial scans shouldn't make a difference, but I thought I should > mention it just in case). > > Of course I can simply coregister this participant by hand, but it would be > more satisfying to understand why it is going awry. Any suggestions? > > thanks, > > Brian > > > -- > Brian Murphy > Post-Doctoral Researcher > Language, Interaction and Computation Lab > Centre for Mind/Brain Sciences > University of Trento > http://clic.cimec.unitn.it/brian/ >