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:
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:
Could anyone guide us into what it may be happening.
Thanks in advance!
Version:
0.7.2
Environment (Docker, Singularity / Apptainer, custom installation):
Docker