Warp native-space tedana derivatives to standard space with fMRIPrep transforms.

fmriprep_warp.sh

# First, let's define some paths to the fMRIPrep and tedana outputs
fmriprep_dir="/path/to/fmriprep/derivatives/of/subject"
tedana_dir="/path/to/tedana/derivatives"

# Result of denoising the scanner-space multi-echo data with tedana
file_to_warp="${tedana_dir}/sub-01_task-rest_desc-optcomDenoised_bold.nii.gz"

# Name of the standard-space denoised data file to be written out
out_file="${tedana_dir}/sub-01_task-rest_space-MNI152NLin2009cAsym_desc-optcomDenoised_bold.nii.gz"

# An existing standard-space
standard_space_file="${fmriprep_dir}/func/sub-01_task-rest_space-MNI152NLin2009cAsym_boldref.nii.gz"

# Transforms
xform_native_to_t1w="${fmriprep_dir}/func/sub-01_task-rest_from-scanner_to-T1w_mode-image_xfm.txt"
xform_t1w_to_std="${fmriprep_dir}/anat/sub-01_from-T1w_to-MNI152NLin2009cAsym_mode-image_xfm.h5"

antsApplyTransforms \
    -e 3 \
    -i ${file_to_warp} \
    -r ${standard_space_file} \
    -o ${out_file} \
    -n LanczosWindowedSinc \
    -t ${xform_native_to_t1w} \
    ${xform_t1w_to_std}