Non-linear registration with QSIPrep?

Software Support
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1

Summary of what happened:

Hello the Neurostars Community,

My question is pretty general and not related to a specific bug:
Is it possible to perform a non-linear co-registration of DWI with T1w images using QSIprep?

I thought at first that the --force-syn flag would perform a non-linear registration (using it even if I have a fieldmap), but the output HTML let me think that only a rigid or affine registration was done.

Can anyone help me on that subject ? I would really need non-linear registration for my DWI as they come from subjects with high cortex deformation thus linear registration is not sufficient.

Thanks in advance for any help.

Command used:

apptainer run --cleanenv --containall \
                --bind {bids_dir}:/mnt/rawdata:ro \
                --bind {output_dir}:/mnt/work:rw \
                --bind {fs_license_path}:/mnt/license.txt:ro \
                {qsiprep_sif_path} \
                /mnt/rawdata /mnt/work/output/ \
                participant \
                --omp-nthreads 16 --mem 32000 \
                --output-resolution 2 \
                --skip-bids-validation \
                --force-syn \
                --unringing-method mrdegibbs \
                --work-dir /mnt/work/workdir/ \
                --fs-license-file /mnt/license.txt \
                -vv \
                --participant-label {subject_id} \
                --session-id ses-{session} \
                --stop-on-first-crash

Version:

QSIPrep 1.1.1

Environment

HPC run with apptainer

2

Hi @Tolema and welcome to neurostars!

That is not possible in QSIPrep. You can only choose between --b0-to-t1w-transform Rigid or --b0-to-t1w-transform Affine .

Best,
Steven

3

Hi Steven, thank you for clarifying this quickly.
Do you think I could register non-linearly qsiprep outputs with other software ? or do you think it could be detrimental to already pre-processed DWI ?
If yes, do you have any advice to do so properly please?
Best,
Tolema