Summary of what happened:
Hi guys,
I’m looking at cerebral blood flow maps generated with ASLprep, and I see values around 10 inside the ventricular regions for basically all images. Is this normal?
Command used (and if a helper script was used, a link to the helper script or the command generated):
#Define subject list
SUBJECT_LIST=/home/m/mchakrav/cindylu/scratch/analysis/ASLprep/subject_list.txt
SUBJECT=$(sed -n "${SLURM_ARRAY_TASK_ID}p" $SUBJECT_LIST)
export FS_LICENSE=/home/m/mchakrav/cindylu/scratch/analysis/ASLprep/freesurferlicense/license.txt
export TEMPLATEFLOW_HOME=/home/m/mchakrav/cindylu/scratch/analysis/templateflow
export APPTAINERENV_FS_LICENSE=/freesurfer_license/license.txt
export APPTAINERENV_TEMPLATEFLOW_HOME=/templateflow
singularity run --cleanenv \
--env TEMPLATEFLOW_HOME=/templateflow \
--bind /home/m/mchakrav/cindylu/scratch/analysis/ASLprep/bids_hcp_aging_dataset:/data:ro \
--bind /home/m/mchakrav/cindylu/scratch/analysis/ASLprep/output:/out \
--bind /home/m/mchakrav/cindylu/scratch/analysis/ASLprep/intermediatefiles:/work \
--bind /home/m/mchakrav/cindylu/scratch/analysis/ASLprep/freesurferlicense:/freesurfer_license \
--bind /home/m/mchakrav/cindylu/scratch/analysis/templateflow:/templateflow \
/home/m/mchakrav/cindylu/scratch/analysis/ASLprep/aslprep-0.7.5rc2.simg \
/data /out participant \
--participant-label ${SUBJECT} \
--skip_bids_validation \
--output-spaces T1w MNI152NLin2009aSym \
--basil \
--fs-license-file /freesurfer_license/license.txt \
--work-dir /work
Version:
aslprep_0.7.5rc2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
