Hello,
I am using ICA-AROMA for motion artefact removal as described in the original Pruim 2015 paper. I minimally preprocess my functional data using the feat gui: motion correction, estimation of linear and nonlinear warping parameters for registration of functional to MNI space (the usual: T1 to EPI with FLIRT and EPI to MNI with FNIRT), and smoothing. I apply ICA-AROMA in native space, and the output is a denoised functional image in native space. Now, I must re-apply the warping parameters estimated in the initial preprocessing to get this denoised image into MNI 152 space.
Is this the correct pipeline that Pruim et al 2015 proposed (it was unclear to me based on my reading of the paper)?
& Is below the correct code for applying registration with pre-estimated parameters?
applywarp --ref=${FSLDIR}/data/standard/MNI152_T1_2mm --in=${rest_dir}/ICA_AROMA/denoised_func_data_nonaggr.nii.gz --warp=${rest_dir}/reg/highres2standard_warp --premat=${rest_dir}/reg/example_func2highres.mat --out=${rest_dir}/ICA_AROMA/warped_denoised_func_data_nonaggr.nii.gz
Thanks all,
Dina Dajani
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