Hi NeuroStars,
I’m currently using QSIPrep to preprocess my DWI data. My goal is to bring ROIs defined in MNI2009c space into native DWI space (MNI → T1w → DWI) in order to overlay the transformed masks on subject-specific FA maps and ensure that the ROIs are well-aligned with white matter. I understand that QSIprep outputs are ACPC-aligned and that the dwiref image is already coregistered with the T1w reference, but for the overlay, I need them to be in the same voxel space and resolution, which requires applying the appropriate transforms.
As mentioned in the QSIprep documentation, the final QSIPrep outputs do not yet include transforms for the coregistration between dwiref and T1w. Within the qsiprep_wf, I noticed a potential affine .mat file inside the b0_to_anat folder. However, it appears to use an intermediate b0 reference image (eddy_corrected_LPS_b0_series_mean) that differs from the final dwiref outputted in the qsiprep main folder ( sub-XX_space-ACPC_dwiref.nii.gz). As a result, applying this transform directly doesn’t work as expected (the result is misaligned). I was wondering if it might be because some additional steps and transformations were applied to dwiref after the coregistration.
Am I missing a relevant transform file or reference image that would make this registration step easier? Or the way to proceed would be to manually register dwiref to T1w if further ROI work is needed?
Thanks for any clarification, and apologies if I’ve overlooked something obvious!
Command used (and if a helper script was used, a link to the helper script or the command generated):
docker run -ti --rm \
-v /path/to/BIDS_dataset:/data:ro \
-v /path/to/output_dir:/out \
-v /path/to/working_dir:/work \
pennlinc/qsiprep:latest /data /out participant \
--participant-label sub-XX \
--output-resolution 1.3 \
--fs-license-file /path/to/license.txt \
--unringing-method mrdegibbs \
--dwi-denoise-window 5 \
--nthreads 8 \
--omp-nthreads 8 \
-w /work