ASLPrep not recognizing field maps

Software Support
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1

Summary of what happened:

Hi everyone. I’m attempting to use ASLPrep 25.1.0 to process 2D multi-band PCASL data gathered using the CMRR sequence, but it doesn’t seem to recognize the accompanying spin-echo field maps. I have tried multiple fixes based on other forum posts here, but unfortunately none have worked so far.

I have data from three participants, some with multiple runs, set up in the following way:

sub-XX/ses-XX/perf/sub-XX_ses-XX_dir-PA_run-01_asl.nii.gz
sub-XX/ses-XX/perf/sub-XX_ses-XX_dir-PA_run-01_asl.json

sub-XX/ses-XX/fmap/sub-XX_ses-XX_dir-AP_run-01_epi.nii.gz
sub-XX/ses-XX/fmap/sub-XX_ses-XX_dir-AP_run-01_epi.json
sub-XX/ses-XX/fmap/sub-XX_ses-XX_dir-PA_run-01_epi.nii.gz
sub-XX/ses-XX/fmap/sub-XX_ses-XX_dir-PA_run-01_epi.json

The fmap JSONs contain the following (among other fields):

"PhaseEncodingDirection": "j-",
"TotalReadoutTime": 0.0484496,
"IntendedFor": ["ses-XX/perf/sub-XX_ses-XX_dir-PA_run-01_asl.nii.gz"]

Where j- is used for the AP fmap and j is used for the PA fmap. The perfusion data also includes the field PhaseEncodingDirection: j.

I have tried a few fixes already, including adding or removing the BIDS URI (bids::sub-XX/) in the IntendedFor field, adding or removing brackets around the IntendedFor field, and adding

"B0FieldIdentifier": "fmap1"
"B0FieldSource": "fmap1"

to the fmap and perfusion JSONs, respectively. The online BIDS validator gives errors regarding a few missing keys (BackgroundSuppression, SkullStripped, and TotalAcquiredPairs), but otherwise nothing about field maps. I am running ASLPrep via singularity in Ubuntu via a bash script with the command below:

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

$(singularity run \
	--cleanenv \
	--bind ${BIDSINDATA}:/SubjectsMBPCASL_25.1.0 \
	--bind ${BIDSOUTDATA}:/SubjectsMBPCASL_25.1.0_derivatives \
	--bind /home/Software/FreeSurfer/freesurfer-7.3.2/freesurfer:/fs_license \
	--bind /nox2/data/aslprep_workdir_tmp:/workdir \
	/home/Software/aslprepS-25.1.0 \
	--skip_bids_validation \
	/SubjectsMBPCASL_25.1.0 \
	/SubjectsMBPCASL_25.1.0_derivatives \
	participant \
	--participant_label ${SUBJECT} \
	-w /workdir/work_sub-${SUBJECT} \
	--output-spaces MNI152NLin6Asym:res-2 anat fsaverage \
	--omp-nthreads 2 \
	--nthreads 4 \
	--mem-mb 96000 \
	--fs-license-file /fs_license/license.txt \
	&> ${LOGDIR}/aslprepS_25.1.0_MBPCASL_Site_${SITE}_${SUBJECT}_${DATEF}.log) &

Version:

ASLPrep 25.1.0

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

Singularity

Data formatted according to a validatable standard? Please provide the output of the validator:

See screenshot below.

Relevant log outputs (up to 20 lines):

251209-11:03:29,858 nipype.workflow INFO:
	 Collected run data for /SubjectsMBPCASL_25.1.0/sub-XX/ses-XX/perf/sub-XX_ses-XX_dir-PA_run-01_asl.nii.gz:
aslcontext: /SubjectsMBPCASL_25.1.0/sub-XX/ses-XX/perf/sub-XX_ses-XX_dir-PA_run-01_aslcontext.tsv
m0scan: null
sbref: null

251209-11:03:29,871 nipype.workflow INFO:
	 No single-band-reference found for sub-XX_ses-XX_dir-PA_run-01_asl.nii.gz.
251209-11:03:29,956 nipype.workflow INFO:
	 Stage 1: Adding HMC aslref workflow
251209-11:03:29,961 nipype.workflow INFO:
	 Stage 2: Adding motion correction workflow
251209-11:03:29,966 nipype.workflow INFO:
	 No fieldmap correction - skipping Stage 3

Screenshots / relevant information:

BIDS Validator:

image
image2273×817 34.4 KB

The dcm2bids JSON file includes:

{
    "id" : "mbPCASL_PA_01",
    "datatype": "perf",
    "suffix": "asl",
    "custom_entities": "dir-PA",
    "criteria": {
	"SeriesDescription": "mbPCASLhr_PA_01"
    },
    "sidecar_changes": {
		"ArterialSpinLabelingType": "PCASL",
		"PostLabelingDelay": 1.64186,
		"LabelingDuration": 1.5,
		"M0Type": "Included",
		"RepetitionTimePreparation": 3.58,
		"B0FieldSource": "fmap1"
    }
},
	{
    "datatype": "fmap",
    "suffix": "epi",
    "custom_entities": "dir-PA",
    "criteria": {
	"SeriesDescription": "PCASLhr_SpinEchoFieldMap_PA_01"
    },
    "sidecar_changes" : {
	"IntendedFor" : [
	    "mbPCASL_PA_01"
	],
	"B0FieldIdentifier": "fmap1"
    }
},
{
    "datatype": "fmap",
    "suffix": "epi",
    "custom_entities": "dir-AP",
    "criteria": {
	"SeriesDescription": "PCASLhr_SpinEchoFieldMap_AP_01"
    },
    "sidecar_changes" : {
	"IntendedFor" : [
	    "mbPCASL_PA_01"
	],
	"B0FieldIdentifier": "fmap1"
    }
},

Thanks for the help!

Keith G. Jones
Department of Psychiatry and Biobehavioral Sciences
University of California, Los Angeles

2

Hi @kgjones,

Can you provide the contents of your dataset_description.json? In particular, want to make sure the DatasetType is "raw".

Best,
Steven

1 Like
3

Hi Steven,

Thanks for the quick response! It does appear that the dataset_description.json file was the issue. I copied an old file over to use with these tests scans, and I mistakenly took one from a derivatives folder, so the DatasetType was incorrect. Everything appears to be working now. Thanks again!

Keith G. Jones
Department of Psychiatry and Biobehavioral Sciences
University of California, Los Angeles

1 Like