Hi experts,
I am trying to take the AAL UNC neonatal atlas (adapted into dHCP extdhcp40wk space) and transform it into native diffusion space to be used in probabilistic tractography for the dHCP dataset.
dHCP provides the warp files for extdhcp40wk to diffusion space transformations (xfm/${sub}_${ses}_from-extdhcp40wk_to-dwi_mode-image.nii.gz). However, I am having difficulties getting the transformation to work successfully.
I saw this thread on transforming data using warp files, so I tried that command in Connectome Workbench:
wb_command -volume-warpfield-resample derivatives/UNCatlas/AAL_UNCneo_in_extdhcp40wk.nii.gz fmriresults01/rel3_derivatives/rel3_dhcp_dmri_shard_pipeline/${sub}/${ses}/xfm/${sub}_${ses}_from-extdhcp40wk_to-dwi_mode-image.nii.gz derivatives/mrtrix/${sub}/dwi/${sub}_mean1000.nii.gz ENCLOSING_VOXEL derivatives/UNCatlas/${sub}/${sub}_wb_UNC.nii.gz -fnirt derivatives/UNCatlas/AAL_UNCneo_in_extdhcp40wk.nii.gz
I am leveraging a mean b-shell of 1000 for the transformation, as that was what was used in the original paper to transform the diffusion data into atlas space. However, the resulting transformation is not good at all.
I am not sure if I am missing something, or if there is a better way to do this. Any thoughts on how to do this transformation properly would be of great help!
Best Wishes,
Katie
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