Summary of what happened:
dcm2niix converted the asl dicoms into two 3D volumes, one of them is the m0 volume, the other is a deltam volume (described as case 2 over here Arterial Spin Labeling - Brain Imaging Data Structure 1.11.1 ). This is unlike the usual 4D volumes with repeated pairings of label and control images.
I tried playing around with the options indcm2niix hoping to obtain the original label control images but to no avail.
I ran aslprep on this deltam volume anyway and i encountered the error below. So i’m wondering if deltam volumes are supported at the moment?
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv \
-B /usr/local/freesurfer-7.4.1/license.txt:/opt/freesurfer/license.txt,$bids_dir,$output_dir,$work_dir,$SUBJECTS_DIR \
$HOME/aslprep \
$bids_dir \
$output_dir \
participant -w "$work_dir"/"$d" \
--skip_bids_validation \
--fs-subjects-dir $SUBJECTS_DIR \
--cifti-output 91k \
--basil \
--aggregate-session-reports 10 \
--skip-parcellation \
--participant-label $d \
--nthreads 6 \
--omp-nthreads 6 \
--md-only-boilerplate
Version:
ASLPrep 26.0.2
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
yes
PASTE VALIDATOR OUTPUT HERE
Relevant log outputs (up to 20 lines):
260726-23:33:24,691 nipype.workflow ERROR:
Node extract_3d_asl failed to run on host hpc-wfly-rvf002.
260726-23:33:24,694 nipype.workflow ERROR:
Saving crash info to /scratch/junhong.yu/ADNI/output/sub-0050602/ses-bl/log/20260726-232929_0efa055b-8d5c-4861-ab8e-df885e256428/crash-20260726-233324-junhong.yu-extract_3d_asl-4087e06b-8334-4018-bc45-d3eef3346ea1.txt
Traceback (most recent call last):
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 525, in run
result = self._run_interface(execute=True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 643, in _run_interface
return self._run_command(execute)
^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nipype/pipeline/engine/nodes.py", line 769, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node extract_3d_asl.
Traceback:
Traceback (most recent call last):
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nipype/interfaces/base/core.py", line 401, in run
runtime = self._run_interface(runtime)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/aslprep/interfaces/utility.py", line 390, in _run_interface
img_3d = index_img(self.inputs.in_file, self.inputs.index)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nilearn/image/image.py", line 829, in index_img
imgs = check_niimg_4d(imgs)
^^^^^^^^^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nilearn/image/image.py", line 2497, in check_niimg_4d
return check_niimg(
^^^^^^^^^^^^
File "/app/.pixi/envs/aslprep/lib/python3.12/site-packages/nilearn/image/image.py", line 2393, in check_niimg
raise DimensionError(len(niimg.shape), ensure_ndim)
nilearn.exceptions.DimensionError: Input data has incompatible dimensionality: Expected dimension is 4D and you provided a 3D image. See https://nilearn.github.io/stable/manipulating_images/input_output.html.