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Thank you Stephen, Even the functional image after registration to MNI appears large. I attached an image (the functional image in red). The areas of the functional image that do not overlap the MNI appear to have lower intensities (as seen in fslview) compared to the areas in the middle that overlap the standard image. Might that have anything to do with the problem? Thanks a lot Helen ________________________________ From: FSL - FMRIB's Software Library [[log in to unmask]] On Behalf Of Stephen Smith [[log in to unmask]] Sent: Tuesday, April 09, 2013 5:26 PM To: [log in to unmask] Subject: Re: [FSL] problem with registration Hi - you need to also look at the standard-space aligned FMRI images - are they all well aligned? It may just be that you have liberal masking/betting, meaning that the data processed in standard space is liberal compared with the MNI152 mask/brain. If this happens it's not surprising that you could get some MELODIC components corresponding to FoV issues, but that shouldn't be a problem for the majority of the within-brain components. Cheers. On 9 Apr 2013, at 15:15, Helen Sawaya <[log in to unmask]<mailto:[log in to unmask]>> wrote: Dear fsl experts, I am running a group analysis in MELODIC and I have a problem with registration of my functional images. The sum of all masks after registration to MNI (the mask image in the .gica folder) appears larger than the standard MNI. I attached a picture of maskunique- we could see that the dashed-colored line does not overlap the standard image. I am therefore getting activations outside the brain. But I can't seem to be able to specify a single bad functional image. I used robust BET to extract non brain areas of the functional images. I then preprocessed them in FEAT, denoised them using fsl_regfilt and inputted the denoised images in melodic where I registered them to T1 and MNI and ran group ICA. Is the problem likely to be in the brain extraction procedure? What could explain this 'halo' in maskunique that is larger than the MNI image? Your input is much appreciated Thank you!! Helen <maskunique_overlay.png> --------------------------------------------------------------------------- Stephen M. Smith, Professor of Biomedical Engineering Associate Director, Oxford University FMRIB Centre FMRIB, JR Hospital, Headington, Oxford OX3 9DU, UK +44 (0) 1865 222726 (fax 222717) [log in to unmask]<mailto:[log in to unmask]> http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------