Hi Jon,

This would be because you are using a linear registration; the result is not poor, it is simply limited by the fact that it is affine. Try using TBSS instead (that uses non-linear registration).

Cheers,Gwenaëlle
 
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Gwenaëlle Douaud, PhD
Associate Professor & MRC Career Development Fellow

FMRIB Centre, University of Oxford
John Radcliffe Hospital, Headington
OX3 9DU Oxford UK
Switchboard: +44 (0) 1865 222 493
Fax: +44 (0) 1865 222 717

www.fmrib.ox.ac.uk/team/principal-investigators/gwenaelle-douaud
www.fmrib.ox.ac.uk/research/translational-image-analysis-group
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De : Jon Anderson <[log in to unmask]>
À : [log in to unmask]
Envoyé le : Vendredi 29 juillet 2016 12h25
Objet : [FSL] Registering FA maps to FMRIB58

Dear Experts,
What is the correct method to register FA maps to FMRIB58 space?
I tried to use the command flirt as follow:

flirt -in FA_MAP.nii.gz -ref /autofs/cluster/pubsw/2/pubsw/Linux2-2.3-x86_64/packages/fsl.64bit/5.0.7/data/standard/FMRIB_58.nii.gz -out FA_MAP.FMRIB.nii.gz -omat FA_MAPS.FMRIB.mat -bins 256 -cost corratio -searchrx -90 90 -searchry -90 90 -searchrz -90 90 -dof 12  -interp trilinear &

The results was totally depressing. When I merge the resultant FA maps ( using fslmerge -t ... ), I see that all of these registered FA maps are in FMRIB58 but they are not matching with each other ( the registration is very poor).

Any suggestions to get the optimal and best registration between these FA maps and FMRIB58 are highly appreciated.

Thanks in advance
Jon