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Dear Stephen The images (example func, T1, and field map) all start with the same orientation. Filed map correction worked very well using the same input images in fsl4, but not fsl 5.0.1. Is there any way I can upload more information for you? The mailing list doesn’t allow more than 200kb attachments at a time. Best wishes Fatemeh Dr Fatemeh Geranmayeh Wellcome Trust Clinical Research Fellow The Computational, Cognitive and Clinical Neuroimaging Laboratory Imperial College London Telephone : 020 7594 7994 From: Stephen Smith <[log in to unmask]<mailto:[log in to unmask]>> Reply-To: FSL - FMRIB's Software Library <[log in to unmask]<mailto:[log in to unmask]>> Date: Sun, 4 Nov 2012 07:31:14 +0000 To: <[log in to unmask]<mailto:[log in to unmask]>> Subject: Re: [FSL] difficulties with FSL5 using BBR and filed map correction Hi - it looks like the alignment of the fieldmaps to the functional data may be poor, but it's hard to see from the lowres images you sent - is that a possibility? Did all the different kinds of images start with the right/same orientation? Cheers. On 2 Nov 2012, at 19:07, Geranmayeh, Fatemeh wrote: Dear experts I loaded a design.fsf file from a previously run analysis in FSL4 that contained field map correction and FLIRT registration into FSL 5. I then re ran the same first level analysis with FSL 5 and BBR option (not making any other changes, for example no changes to B0 unwrapping option),however it appears that the field map correction makes the distortions much worse when used in FSL 5. (see attached files). I have also attached the design.fsf file. I checked the analysis with a different patient who had less atrophy, but the problem persists. Any advise will be much appreciated and I am happy to send more files (there was a limit of 200 K on this email) Many thanks Fatemeh Dr Fatemeh Geranmayeh Wellcome Trust Clinical Research Fellow The Computational, Cognitive and Clinical Neuroimaging Laboratory Imperial College London Telephone : 020 7594 7994 <field map FSL 4.pdf.zip><design.fsf_FSL5.zip><field map _FSL 5 .pdf.zip> --------------------------------------------------------------------------- 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 ---------------------------------------------------------------------------