Summary of what happened:
Hi,
I processed a test subject with and without the --longitudinal flag. I was reviewing the CITATION.md file (thank you for that file, is great to have such details), and both files display identical information regarding “anatomical data processing”. I found some differences in the visual report, particularly impacting the brain template and brain tissue segmentation. Also found high CBF values for WM in the BASIL CBF by tissue plot across sessions, and higher CBF values for WM in BASIL GM-PVC CBF by tissue type (when using the --longitudinal flag)
All three sessions available for this subject were fully processed regardless of the flag, so I wonder, could you provide further information on the impact of using the flag? Specially any special considerations to keep in mind when looking at the CBF maps?
Command used (and if a helper script was used, a link to the helper script or the command generated):
About
ASLPrep command: /opt/conda/envs/aslprep/bin/aslprep /data /out participant --participant-label XX --skip_bids_validation --n_cpus 16 --output-spaces T1w MNI152NLin2009aSym fsaverage fsLR --longitudinal --random-seed 42 --basil --aggregate-session-reports 3 --skull-strip-fixed-seed --medial-surface-nan --project-goodvoxels --cifti-output 91k --fs-license-file /freesurfer_license/license.txt -vv --resource-monitor --write-graph --work-dir /work
Date preprocessed: 2025-11-12 07:28:53 -0500
and
ASLPrep command: /opt/conda/envs/aslprep/bin/aslprep /data /out participant --participant-label XX --skip_bids_validation --n_cpus 16 --output-spaces T1w MNI152NLin2009aSym --random-seed 42 --basil --aggregate-session-reports 3 --skull-strip-fixed-seed --fs-license-file /freesurfer_license/license.txt -vv --resource-monitor --write-graph --work-dir /work
Date preprocessed: 2025-11-12 06:40:10 -0500
Version:
ASLPrep version: 25.1.0
Environment (Docker, Singularity / Apptainer, custom installation):
Apptainer
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:
BASIL GM-PVC CBF by Tissue Type with --longitudinal flag (session 1)
BASIL GM-PVC CBF by Tissue Type without --longitudinal flag (session 1)
