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Dear Fatemeh, It is possible to use fieldmaps with lesion masks and we would encourage it. The difficulty is checking that all the intermediate registrations are fine. There are a few things you should check: - that the fieldmap does not contain any artefact in the lesion areas - that the registration of the fieldmap magnitude to the example_func looks OK - that the example_func to structural registration looks OK Assuming that these are OK (and ideally these should be fine with lesions as the lesions will be present in all images of that subject) then the strategy you propose (using the lesion mask for the structural to standard registration) should work fine. All the best, Mark On 1 Aug 2012, at 12:57, Geranmayeh, Fatemeh wrote: > Thank you very much for this. > > I have a few more questions please. Is it valid/possible to use a) field > map correction and/or b) FNIRT in conjunction with lesion masking in > stroke patients? > > At the moment I am using field map correction with FNIRT to register older > control brains to standard MNI space. My registration is not great at the > frontal, occipital and temporal poles, resulting in activation a few > millimetres outside the brain in these focal regions. This problem is > particularly worse with my stroke group with left hemisphere lesions, > which I am masking out in the registration. With the patient group I do a > two stage registration: First, I run FLIRT as part of the FEAT cascade; > Second, I updatefeatreg (use the FLIRT to register the T1 to standard > brain with the mask (inverse) as input weighting volume, then concatenate > the transformation matrices, and apply it to the example_func and finally > updatefeatreg). > > My first question above (a) is : Is it valid to use field map correction > in stage 1 of the patient registration, before updating the feat reg > folder? > > > 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 > > > > > > On 24/07/2012 18:04, "Mark Jenkinson" <[log in to unmask]> wrote: > >> Hi, >> >> This is going to be in our upcoming release, but in the meantime you can >> find a copy of fsl_prepare_fieldmap at: >> http://www.fmrib.ox.ac.uk/fsldownloads/patches/ >> >> This just needs to be copied to $FSLDIR/bin/ on your machine. >> Note that this is only designed to work with Siemens data at present. >> >> All the best, >> Mark >> >> >> On 24 Jul 2012, at 13:57, Fatemeh Geranmayeh wrote: >> >>> Dear Experts. >>> >>> I am following the instructions given at 2012 FSL course on how to >>> process fieldmap phase difference images acquired by Siemens. ( Page 286 >>> of the handout). The command fsl_prepare_fieldmap does not work, and I >>> can not get the usage command by just typing it either. I note someone >>> else raised this issue back in May. I have tried both >>> fsl_prepare_fieldmap, and prepare_fieldmap command. There are no manual >>> /help entry for this. >>> >>> >>> Can you help? >>> >>> Best wishes >>> Fatemeh >>> >