Dear Max,

your problem is very likely with acquisition (check your raw data), and 
not image processing. Close to air-tissue transitions EPI suffers from 
magnetic field inhomogeneities, leading to increased dephasing of your 
spins and thus a fast drop of transversal magnetization. That is why you 
see it on top of the sinuses and over the middle/inner ear.

This is a very well known problem of EPI fMRI. You could consult your MR 
physicist how to decrease the size of these dropout regions (short TE, 
thinner slices, SENSE or GRAPPA, etc), but they will always be there to 
some extent. Nothing much you can do about that.

Good luck,


On 05/31/2011 11:08 PM, Max Hilger wrote:
> Dear SPM-Users,
> we are currently doing a fMRT analysis in SPM8. The preprocessing of our images consists of realignment, slice timing, normaization to the EPI-template and smoothing.
> When we checked the results by overlaying the EPI-template with the activation maps after preprocessing in MRIcro we noticed that for all the subjects there seems to be a consitent lack of activation in certain regions.
> The images attached are typical for all subjects analized. As you can see there seems to be a "hole" in the activation in the temporal lobe (bilateral, upper images) and in the inferior frontal lobe (lower images). The size of these gaps in activation seems to differ slightly across the subjects, but the general pattern is pretty consistent.
> It would be very nice if you could give me insight what went wrong with the preprocessing and help solve this problem. IF needed I can of course provide additional info regarding the parameters used.
> Thanks in advance for any input!
> Best regards,
>   Max Hilger

Dr. S.F.W. Neggers
Division of Brain Research
Rudolf Magnus Institute for Neuroscience
Utrecht University Medical Center
Visiting: Heidelberglaan 100, 3584 CX Utrecht
           Room B.01.1.03

Mail    : Huispost B.01.206, P.O. Box 85500
           3508 GA Utrecht, the Netherlands
Tel     : +31 (0)88 7559609
Fax     : +31 (0)88 7555443
E-mail  : [log in to unmask]
Web     :