Hello,

You can calculate the registration matrix using FLIRT and the flag -omat to get the matrix:

flirt [options] -in <inputvol> -ref <refvol> -omat <outputmatrix>

 

You can also combine different transformations in case you have them available from previous steps. For example if you have already calculated the transformation from FLAIR to T1 and from T1 to MNI (and you are using FLAIR as your base image for BIANCA), you can combine them as described here:

https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/FAQ#How_do_I_do_a_two-stage_registration_using_the_command_line.3F

 

Hope it helps,

Ludovica

 

Ludovica Griffanti, PhD
Alzheimer's Association Research Fellow
Wellcome Centre for Integrative Neuroimaging (WIN)
Department of Psychiatry | Nuffield Department of Clinical Neurosciences
University of Oxford
email: [log in to unmask]
Please don’t feel obliged to read or respond to my email outside your own working hours

 

 

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