Hi Sam,
Try using epi_reg (https://fsl.fmrib.ox.ac.uk/fsl/fslwiki/FLIRT/UserGuide#epi_reg)
Vale,
Tibor
Auer, Tibor M.D. Ph.D.
Research Fellow in MRI
Department of Psychology
Royal Holloway University of London
Egham Hill
Egham
TW20 0EX
United Kingdom
+44-1784-27-6594
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@TiborAuer
-----Original Message-----
From: FSL - FMRIB's Software Library <[log in to unmask]> On Behalf Of Sam W.
Sent: Friday, January 18, 2019 9:31 PM
To: [log in to unmask]
Subject: [FSL] registration using the command line
Hello,
I'm trying to mimic the behavior of FEAT using the command line but I'm not sure how to do the registration step. Assuming I already did motion correction and slice timing, how can I now register my functional data to the anatomical image to MNI template using flirt/fnirt combination as in FEAT?
I found this code in the FSL fnirt page:
bet my_structural my_betted_structural
flirt -ref my_betted_structural -in my_functional -dof 6 -omat func2struct.mat flirt -ref ${FSLDIR}/data/standard/MNI152_T1_2mm_brain -in my_betted_structural -omat my_affine_transf.mat fnirt --in=my_structural --aff=my_affine_transf.mat --cout=my_nonlinear_transf --config=T1_2_MNI152_2mm applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=my_functional --warp=my_nonlinear_transf --premat=func2struct.mat --out=my_warped_functional
but I don't think this will give me the same result as FEAT, will it? For example FEAT uses BBR which is not specified in the flirt command.
Thank you very much,
Sam
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