ASLprep alignment of anatomical and functional data

Software Support
1

Hello,

Summary of what happened

We have ran ASLprep (v.0.7.2) on our data.

Command used (and if a helper script was used, a link to the helper script or the command generated):

aslprep \
    neurodesktop-storage/Agueda/BIDS \
    neurodesktop-storage/Agueda/BIDS/derivatives/aslprep \
    participant \
    --participant-label sub-897\
    --force-bbr \
    --basil \
    --ignore t2w \
    --fs-subjects-dir /Users/heartybrain/neurodesktop-storage/heartybrain/BIDS/derivatives/freesurfer/sourcedata/freesurfer_pre/sourcedata \
    --bids-filter-file neurodesktop-storage/heartybrain/BIDS/BIDS_filter_file.json \
    --fs-license-file neurodesktop-storage/heartybrain/BIDS/license.txt \
    -vv \
    -w neurodesktop-storage/heartybrain/BIDS

When inspecting outputs we found out that alignment between ASL and anatomical data was not perfect for all participants, example below:

Captura de pantalla 2024-12-19 a las 10.43.14
Captura de pantalla 2024-12-19 a las 10.43.141920×896 113 KB

When decided then to rerun one participant to check if it was an error of preexisting freesurfer outputs, or because of using --force-bbr, however it still did not look perfect.

Command used (and if a helper script was used, a link to the helper script or the command generated):

aslprep \
    neurodesktop-storage/Agueda/BIDS \
    neurodesktop-storage/Agueda/BIDS/derivatives/aslprep \
    participant \
    --participant-label sub-897\
    --basil \
    --fs-no-reconall \
    --ignore t2w \
    --bids-filter-file neurodesktop-storage/heartybrain/BIDS/BIDS_filter_file.json \
    --fs-license-file neurodesktop-storage/heartybrain/BIDS/license.txt \
    -vv \
    -w neurodesktop-storage/heartybrain/BIDS

Results below:

Captura de pantalla 2024-12-19 a las 10.44.32
Captura de pantalla 2024-12-19 a las 10.44.321920×1009 123 KB

Could anyone guide us into what it may be happening.
Thanks in advance!

Version:

0.7.2

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

Docker

2

Hi!! Kindly reminder in case anyone can shed light into this

3

Hi, not an expert but just some suggestions…

  1. did you have a detailed look at the T1 image - do you notice any issues with this image that might have caused the issue?
  2. I notice that you ignored the T2 image. Does it improve anything to include it?
  3. also, why are using the --fs-no-reconall command? Try running without it.

Jen

4

Hi @AustinBipolar! Thanks for your comment. I will provide more info about the context.

  • Our t2w is specific sequence for hippocampus which we believe it won’t improve coregistration.
  • All t1w images have undergone quality check process, so enough quality from those is ensured
  • –fs-no-reconall command was applied as a second option to see whether data coming from freesurfer is the one causing the problem, but still coregistration do not match perfectly.
5

I released a new version of ASLPrep yesterday (0.7.5) with an updated version of sMRIPrep. Would you mind trying out the new version on your problematic subject to see if that fixes the problem?

6

Having tried using v.0.7.5 and we are encountering same problem.

Command used (and if a helper script was used, a link to the helper script or the command generated):

aslprep \
    neurodesktop-storage/heartybrain/BIDS \
    neurodesktop-storage/heartybrain/BIDS/derivatives/aslprep \
    participant \
    --participant-label sub-897\
    --force-bbr \
    --basil \
    --ignore t2w \
    --fs-subjects-dir /Users/heartybrain/neurodesktop-storage/heartybrain/BIDS/derivatives/freesurfer/sourcedata/freesurfer_pre/sourcedata \
    --bids-filter-file neurodesktop-storage/heartybrain/BIDS/BIDS_filter_file.json \
    --fs-license-file neurodesktop-storage/heartybrain/BIDS/license.txt \
    -vv \
    -w neurodesktop-storage/heartybrain/BIDS

Here I show 2 more examples:

Captura de pantalla 2025-01-15 a las 9.31.50
Captura de pantalla 2025-01-15 a las 9.31.501920×903 113 KB

Captura de pantalla 2025-01-15 a las 9.32.40
Captura de pantalla 2025-01-15 a las 9.32.401920×961 123 KB

7

Thanks for trying that.

ASLPrep relies on sMRIPrep and fMRIPrep to create these transforms, so the issue might be better addressed by someone with more experience debugging fMRIPrep’s coregistration (@smeisler?).

The first image seems to have a lot of distortion. Does the distortion correction look alright?

9

I have had a deeper look into outputs and found out that registration.lta resulting from the following command:

mri_coreg --s sub-897 --dof 6 --ftol 1.000000e-04 --linmintol 1.000000e-02 --threads 8 --lta /data/output/aslprep_0_7_wf/sub_897_wf/asl_preproc_ses_1_wf/asl_fit_wf/asl_reg_wf/bbreg_wf/mri_coreg/registration.lta --sep 4 --mov /data/output/aslprep_0_7_wf/sub_897_wf/asl_preproc_ses_1_wf/asl_fit_wf/asl_reg_wf/bbreg_wf/mri_coreg/sub-897_ses-1_desc-coreg_aslref.nii.gz --sd /data/freesurfer

is differing in transform matrix between versions 0.7.3 and 0.7.5, though information from sub-897_ses-1_desc-coreg_aslref.nii.gz and brainmask.mgz is the same when using both versions. Shouldn’t it had been the same result? Anyhow, none version is solving my issue related to corregistration.