Issue with CBF quantification in multi-delay pCASL data with ASLPrep

Claudia_Tarricone · August 19, 2025, 7:04pm

Hi,

I’m running ASLPrep on my multi-delay pCASL data, but I’m encountering a problem with the CBF quantification (both with the standard model and with BASIL). In the resulting CBF maps, there are regions of the brain that appear to be “cut out,” resulting in patchy areas or “holes” in the quantification.
Additionally, when specifying: --output-spaces “MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-1 MNI152NLin6Asym:res-native MNI152NLin2009cAsym:res-native” the results (CBF, ATT, ecc…) are actually only saved in native resolution (3.5x3.5x3.5 mm), not at 1 mm as also requested.

Command used:

singularity exec --cleanenv \
-B ${BIDS_DIR}:/data 
-B ${TEMPLATEFLOW_DIR}:/templateflow \
-B ${WORK_DIR}:/work \
-B $(dirname $FS_LICENSE):/fs_dir \
-B ${FREESURFER_HOST_DIR}:/fs_home \
  /nfsd/opt/sif-images/aslprep.sif \
/opt/conda/envs/aslprep/bin/aslprep /data /data/derivatives/ASLPrep_latest 
participant 
--participant-label Sub002 
--mem 12GB 
--fs-license-file /fs_dir/fs_license.txt 
-w /work 
--asl2anat-dof 6 
--asl2anat-init t2w 
--basil 
--output-spaces MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-1 MNI152NLin6Asym:res-native MNI152NLin2009cAsym:res-native 
--cifti-output 
--skip-bids-validation

Version:

ASLPrep version: 25.0.0rc1

Environment:

Singularity

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):

bids_dir = "/data"
bids_database_dir = "/work/20250819-122801_856deb6a-8b80-4e1d-bc68-326b6f608fa0/bids_db"
bids_description_hash = "879bc419226bfe7eec1ff9e8be8c1373ae29a4fdcfd970b161d233d1b0b8327e"
boilerplate_only = false
sloppy = false
debug = []
aslprep_dir = "/data/derivatives/ASLPrep_latest"
fs_license_file = "/fs_dir/fs_license.txt"
fs_subjects_dir = "/data/derivatives/ASLPrep_latest/sourcedata/freesurfer"
layout = "BIDS Layout: .../data | Subjects: 2 | Sessions: 0 | Runs: 4"
log_dir = "/data/derivatives/ASLPrep_latest/logs"
log_level = 25
low_mem = false
md_only_boilerplate = false
notrack = false
output_dir = "/data/derivatives/ASLPrep_latest"
aggr_ses_reports = 4
output_spaces = "MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-1 MNI152NLin6Asym:res-native MNI152NLin2009cAsym:res-native"
reports_only = false
run_uuid = "20250819-122801_856deb6a-8b80-4e1d-bc68-326b6f608fa0"

Screenshots / relevant information:

CBF quantified with BASIL (space MNI152NLin6Asym, native resolution):

I’m not using distortion correction because the fieldmap-less approach (with T1w) gave me even larger missing regions. We also tried:

running without forcing --asl2anat-init t2w

using --asl2anat-dof 12

but the results did not improve (sometimes they were even worse).

The data are organized according to the BIDS standard, and the ASL mask itself (red contour in the image above) does not appear to have that gap — it only shows up in the CBF quantification.

Do you have any idea where the problems could come from, and how we could resolve the?

Thanks!

Claudia

tsalo · August 19, 2025, 7:41pm

This is one of the most common issues users have with ASLPrep. I am currently investigating a possible cause, which is that N4 bias correction may be introducing odd patterns in data that are already normalized. Can you share the ImageType field from your ASL, M0, and sbref files’ JSONs?

I don’t know what might be causing the issue with the output spaces, but I’d recommend opening a separate topic for that.

Claudia_Tarricone · August 20, 2025, 7:51am

Hi @tsalo

thanks a lot for your reply!
For my ASL and M0 (same acquisition, I only separated M0 afterwards) the field is “ImageType”: [“ORIGINAL”, “PRIMARY”, “ASL”, “NONE”, “ND”, “MOSAIC”]
This field is not included in the JSON of my BIDS dataset, since I didn’t found it as required/recommended by the specification. Do you think it should be explicitly added in order for ASLPrep to handle the data properly?
There is no sbref for our pCASL acquisition, though.

I’m not sure if this could be related to the issue, but I re-ran the same command removing the native resolution outputs, keeping only:

–output-spaces MNI152NLin6Asym:res-1 MNI152NLin2009cAsym:res-1

With this setup, the CBF quantification maps no longer show those holes, and the results look much more reasonable.