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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>


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