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Hi - for registering functional data to structural from the same subject we do not recommend using nonlinear registration (though if you have fieldmaps you should apply fieldmap-based unwarping, e.g. via the FEAT GUI). Hence no need for fnirt. Steve. On 30 Apr 2013, at 09:11, SUBSCRIBE FSL Anonymous <[log in to unmask]> wrote: > Dear all, > > I am quite new with the use of FSL and have been studying the FSL website and email list and trying to figure out how should I progress with my analysis. However, I am not quite sure how to proceed. Eventually, I would like to overlay my functional data over contrast enhanced T1 images without normalizing into standard space. This has been bit confusing for me because most of the examples deal with MNI-templates which I wish not to use. > > I have several image sequences available and have been approaching to register first both T1-images and EPI into T2-space to do the overlay. Data is from brain tumor patients so the registration is sometimes affected by large lesions. > > My questions now are, in which order do you recommend doing my analysis and is it possible to do nonlinear registration and what are your recommendations for using brain extracted data. > > Here is example approach for T1 to T2 space which seems to work fine: > flirt -in T1data -ref T2data -omat T1regT2.mat -out T1regT2_flirted -cost normmi -searchcost normmi > fnirt --inn=T1data --ref=T2data --aff=T1regT2.mat --iout=T1regT2_fnirted --cout=T1regT2_fnirted_MAT > applywarp -r T2data -i T1data -w T1regT2_fnirted_MAT -o T1regT2 > > > For EPI, I have read on one of the emails that I should rather use example_func than mean_func? > > flirt -in mean_func -ref T2data -omat EPIregT2.mat -out EPIregT2_flirted -cost normmi -searchcost normmi > > After this, I am in doubt how to proceed > fnirt --inn=mean_func --ref=T2data --aff=EPIregT2.mat --iout=EPIregT2_fnirted --cout=EPIregT2_fnirted_MAT > applywarp -r T2data -i filtered_func_data -w EPIregT2_fnirted_MAT -o EPIregT2 > > or should I just > flirt -in filtered_func_data -ref T2data -applyxfm -init EPIregT2.mat -o EPIregiT2 > and then perform my analysis on the data after the registration and overlay the analysed data with T1regT2 afterwards? > > Thank you in advance! Hopefully I was clear enough on my questions. > --------------------------------------------------------------------------- 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] http://www.fmrib.ox.ac.uk/~steve ---------------------------------------------------------------------------