QSIPrep not outputting MNI152NLin2009cAsym files despite transformation files

Software Support
1

Summary of what happened:

Hi QSIPrep community,

I’m a beginner with QSIPrep, and I’m running into an issue where I’m not getting output files in MNI152NLin2009cAsym space, even though transformation files to MNI152 are generated. I need MNI-normalized outputs for group-level comparisons, and I might be missing something obvious, so I’d appreciate any guidance!

I expected QSIPrep to output T1w and DWI files in space-MNI152NLin2009cAsym (e.g., sub-100_space-MNI152NLin2009cAsym_desc-preproc_T1w.nii.gz, sub-100_ses-blSKYRA_space-MNI152NLin2009cAsym_desc-preproc_dwi.nii.gz), but I only see files in space-ACPC. However, transformation files to MNI152 are generated, suggesting normalization was computed but not applied.

Some of the key files I get:

sub-100_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5
sub-100_from-MNI152NLin2009cAsym_to-ACPC_mode-image_xfm.h5
sub-100_space-ACPC_desc-preproc_T1w.nii.gz
sub-100_space-ACPC_desc-brain_mask.nii.gz
sub-100_ses-blSKYRA_space-ACPC_desc-preproc_dwi.nii.gz
sub-100_ses-blSKYRA_space-ACPC_desc-preproc_dwi.bval
sub-100_ses-blSKYRA_space-ACPC_desc-preproc_dwi.bvec

So I guess my question would be why aren’t MNI152-normalized files being output despite the presence of transformation files (e.g., sub-100_from-ACPC_to-MNI152NLin2009cAsym_mode-image_xfm.h5)?

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/data:/data:ro \
    -v /path/to/output:/out:rw \
    -v /path/to/freesurfer/license.txt:/opt/freesurfer/license.txt:ro \
    -w /path/to/working/dir \
    pennlinc/qsiprep:latest \
    /data /out participant \
    --participant-label sub-100 \
    --denoise-method dwidenoise \
    --pepolar-method TOPUP \
    --output-resolution 2.0 \
    --fs-license-file /opt/freesurfer/license.txt \
    | tee /path/to/qsiprep_sub-100_log.txt

Version:

QSIPrep Version: pennlinc/qsiprep:latest (1.0.1)

Environment (Docker, Singularity / Apptainer, custom installation):

Docker

Data formatted according to a validatable standard? Please provide the output of the validator:

PASTE VALIDATOR OUTPUT HERE

Relevant log outputs (up to 20 lines):

PASTE LOG OUTPUT HERE

Screenshots / relevant information:

2

Hi @gerard and welcome to neurostars!

In the future please use the software support post category template to organize your post. You can see I edited it for you this time.

QSIPrep does not output MNI outputs. You can apply your MNI XFM to the T1w, but we do not recommend applying spatial transformations to the DWI itself as it introduces additional data interpolation and warrants rotating and scaling gradient information. It is also just computationally much more efficient to interpolate your derivatives compared to whole DWI timeseries.

QSIRecon can spatially normalize your derivatives though (e.g. FA maps). See the template_map part of the recon specs (for example here: qsirecon/qsirecon/data/pipelines/test_scalar_maps.yaml at main · PennLINC/qsirecon · GitHub)

Best,
Steven

3

Hi @Steven,

Thank you very much for your help!

Best,
Gerard