Summary of what happened:
Hello I’m a student for studying brain science
I want to run fMRIPrep on singularity because my personal desktop is a high-end computer. So I ran fmriprep on singularity (used command is below) but an error occurs consistently. Only normalization can’t be run.
Command used (and if a helper script was used, a link to the helper script or the command generated):
singularity run --cleanenv /home/park/Desktop/files/fmriprep-23.1.4.simg \
data/bids_root/ out/ \
participant \
--participant-label 001 \
--fs-license-file /home/park/Desktop/files/license.txt --fs-no-reconall \
--skip-bids-validation
Version:
23.1.4
Environment (Docker, Singularity / Apptainer, custom installation):
Singularity
Data formatted according to a validatable standard? Please provide the output of the validator:
bids-validator@1.11.0
(node:532365) Warning: Closing directory handle on garbage collection
(Use `node --trace-warnings ...` to show where the warning was created)
1: [WARN] Each _phasediff.nii[.gz] file should be associated with a _magnitude1.nii[.gz] file. (code: 92 - MISSING_MAGNITUDE1_FILE)
./sub-001/fmap/sub-001_phasediff.nii.gz
Please visit https://neurostars.org/search?q=MISSING_MAGNITUDE1_FILE for existing conversations about this issue.
2: [WARN] The Authors field of dataset_description.json should contain an array of fields - with one author per field. This was triggered based on the presence of only one author field. Please ignore if all contributors are already properly listed. (code: 102 - TOO_FEW_AUTHORS)
Please visit https://neurostars.org/search?q=TOO_FEW_AUTHORS for existing conversations about this issue.
3: [WARN] The Name field of dataset_description.json is present but empty of visible characters. (code: 115 - EMPTY_DATASET_NAME)
Please visit https://neurostars.org/search?q=EMPTY_DATASET_NAME for existing conversations about this issue.
Summary: Available Tasks: Available Modalities:
1229 Files, 9.07GB MRI
103 - Subjects
1 - Session
If you have any questions, please post on https://neurostars.org/tags/bids.
Relevant log outputs (up to 20 lines):
File: /home/park/Desktop/NI_2/KSHAP_18bul/rest_msit/derivatives/sub-001/log/20240120-124628_e4ea70e5-8c9d-4f01-8788-cb787502355a/crash-20240120-125152-park-registration.a0-b54bd93e-ae2d-4129-8c34-3b6c04a986ba.txt
Working Directory: /home/park/Desktop/files/work/fmriprep_23_1_wf/single_subject_001_wf/anat_preproc_wf/anat_norm_wf/_template_MNI152NLin2009cAsym/registration
Inputs:
explicit_masking: True
flavor: precise
float: True
initial_moving_transform:
lesion_mask:
moving: T1w
moving_image:
moving_mask:
num_threads: 8
orientation: RAS
reference: T1w
reference_image:
reference_mask:
settings:
template: MNI152NLin2009cAsym
template_resolution:
template_spec:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/plugins/multiproc.py", line 67, in run_node
result["result"] = node.run(updatehash=updatehash)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 527, in run
result = self._run_interface(execute=True)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 645, in _run_interface
return self._run_command(execute)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/pipeline/engine/nodes.py", line 771, in _run_command
raise NodeExecutionError(msg)
nipype.pipeline.engine.nodes.NodeExecutionError: Exception raised while executing Node registration.
Traceback:
Traceback (most recent call last):
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nipype/interfaces/base/core.py", line 397, in run
runtime = self._run_interface(runtime)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 183, in _run_interface
ants_args = self._get_ants_args()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 458, in _get_ants_args
args["fixed_image"] = mask(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/niworkflows/interfaces/norm.py", line 507, in mask
data = in_nii.get_fdata()
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/dataobj_images.py", line 373, in get_fdata
data = np.asanyarray(self._dataobj, dtype=dtype)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 439, in __array__
arr = self._get_scaled(dtype=dtype, slicer=())
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 406, in _get_scaled
scaled = apply_read_scaling(self._get_unscaled(slicer=slicer), scl_slope, scl_inter)
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/arrayproxy.py", line 376, in _get_unscaled
return array_from_file(
File "/opt/conda/envs/fmriprep/lib/python3.10/site-packages/nibabel/volumeutils.py", line 472, in array_from_file
raise OSError(
OSError: Expected 17060042 bytes, got 945364 bytes from object
- could the file be damaged?
Screenshots / relevant information:
How can I fix this error? Thank you for your attention.